QMMM Tutorial Ws10 11

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CP/MM TutorialGRS, WS 2010/2011Emiliano Ippoliti: [email protected]

We want to study the effect of the solvent (water) and the temperature on the dipolemoment of anacetone molecule. To accomplish that we will resort to several differentsoftware (MOLDEN, CPMD, VMD, Gaussian09, Amber, GROMOS, etc) in order tolet you taste the everyday working in the biophysical field.

The procedure can be summarized in the following steps:

1. Calculate the dipole moment Dv of acetone in vacuum2. Perform a QM/MM molecular dynamics simulation for the acetone in a

classical water box at room temperature.

3. Calculate the dipole moment D for some random snapshots of this simulationand take the mean value4. Calculate the difference D - Dv

Each file mentioned in this tutorial (in bold) can be found in the folder:

/work/Tutorial/ACETONE/

under the subfolder whose name starts with the number of the corresponding sectionof this tutorial.

To do your tests and exercises, work in your own folder that you can create in thedirectory:

/work/Tutorial

by the command: mkdir /work/Tutorial/your_name

Then go to your folder: cd /work/Tutorial/your_name

1 - Where to start?

Acetone is the organic compound with the formula (CH3)2CO. This colorless, mobile,flammable liquid is the simplest example of the ketones:

!"#$%& () Acetone

To obtain an initial structure we use the MOLDEN program1 that can be run simplytyping:

" #$$%&''((()*+,-)./)01'+21340'+21340)#$+1


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/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP is the location where CPMD willlook for the pseudopotentials files which will be specified in the input file. All the pseudopotentials we will use are already present there.

In order to calculate the dipole moment of the acetone in vacuum we first have tooptimize the geometry of the molecule we have constructed in the previous step. So,we need to write an appropriate input file according the syntax of CPMD.3 By yourfavorite editor, write down theopt_geo.inp text file:

&INFOAcetone moleculeGeometry optimization&END

&CPMDOPTIMIZE GEOMETRY XYZCONVERGENCE ORBITALS1.0d-7

CONVERGENCE GEOMETRY7.0d-4&END

&SYSTEMANGSTROMSYMMETRYORTHORHOMBICCELL ABSOLUTE10.6 10.0 9.8 0.0 0.0 0.0CUTOFF70.

&END

&DFTFUNCTIONAL BLYP&END

&ATOMS*C_MT_BLYP.psp KLEINMAN-BYLANDERLMAX=D30.000000 0.000000 0.0000001.367073 0.000000 -0.483333-0.683537 -1.183920 -0.483333

*O_MT_BLYP.psp KLEINMAN-BYLANDERLMAX=D10.000000 0.000000 1.220000

*H_MT_BLYP.psp KLEINMAN-BYLANDERLMAX=P61.367073 0.000000 -1.5723331.880433 0.889165 -0.1203331.880433 -0.889165 -0.120333-0.683537 -1.183920 -1.572333-0.170177 -2.073085 -0.120333-1.710256 -1.183920 -0.120333&END

A BC;D +80/81& #$$%&''((()*%+3)2.7'+80/81)%39


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CPMD Input file

Any CPMD input file is organized in sections that start with &NAME and end with&END. Everything outside those sections is ignored. Also all keywords have to be inupper case or else they will be ignored. The sequence of the sections does not matter,nor does the order of keywords (except in some special case reported in the manual).A minimal input file must have a &CPMD, &SYSTEM, and an &ATOMS section.

This input file starts with an (optional) &INFO section. This section allows you to putcomments about the calculation into the input file and they will be repeated in theoutput file. This can be very useful to identify and match your input and output files.

The first part of &CPMD section instructs the program to do a geometry optimization(XYZ suboption specify you want the final structure also in xyz format in a file calledGEOMETRY.xyz and a trajectory of the optimization in a file namedGEO_OPT.xyz ) with a tight wavefunction and geometry convergence criterionsrespectively (default 10-5 and 5*10-4).

The &SYSTEM section contains various parameters related to the simulation cell andthe representation of the electronic structure. The keywords SYMMETRY, CELL andCUTOFF are required and define the (periodic) symmetry, shape, and size of thesimulation cell, as well as the plane wave energy cutoff (i.e. the size of the basis set),respectively. The keyword ANGSTROM specify that the atomic coordinates and thesupercell parameters and several other parameters are read in ngstroms(pay attention: default is atomic units (a.u.) which are always used internally). Wedefine a primitive orthorhombic cell with the lattice constants obtained by adding 7

in each direction to the dimension of the system: the cell has to be large enough toavoid significant interactions of the acetone molecule and its electron structure withits periodic neighbors. In CPMD all calculations are periodic. Do always aconvergence test looking for example at the total energy value when you increase the box size!

The &DFT section is used to select the density functional (FUNCTIONAL) andrelated parameters. In this case we use the gradient corrected BLYP functional4 (localdensity approximation is the default).

Finally, the &ATOMS section is needed to specify the atom coordinates and the

pseudopotential(s), that are used to represent them. The coordinates are taken fromthe structure written by MOLDEN.The input for a new atom type is started with a ``*'' in the first column. This linefurther contains the file name where to find the pseudopotential information startingin column 2 and several labels as KLEINMAN-BYLANDER, in our case, whichspecifies the method to be used for the calculation of the nonlocal parts of the pseudopotential (this method is extremely efficient but also accurate).The next line contains information on the nonlocality of the pseudopotential: you canspecify the maximuml -quantum number with ``LMAX=l '' where l is S, P or D.5

E 6)D) F4*G4H I)B#4+)C#J>) KL M"KKAN OPELQOPO5R B) S44H T) U807H V)W) C8..H C#J>) V4X) F AYM"KLLN YLOQYLK)


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On the following lines the coordinates for this atomic species have to be given.The first line gives the number of atoms of the current type.---

If you start the geometry optimization (single line):

mpirun -np 8 cpmd.x opt_geo.inp/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP > opt_geo.out &

the calculation should be completed in less than a minute 5 minutes (usetail f opt_geo.out

to monitor the different steps of the calculation reported in the output file).

CPMD Output file

Look at the output file to understand all the information which we can find there.

At the beginning there isthe header where one can see, when the run was started,what version of CPMD was used, and when it was compiled:

PROGRAM CPMD STARTED AT: Tue Jun 1 19:32:59 2010

SETCNST| USING: CODATA 2006 UNITS

****** ****** **** **** ************* ******* ********** *******

*** ** *** ** **** ** ** ***** ** *** ** ** ** ** **** ******* ** ** ** ***** ****** ** ** ** ***

******* ** ** ** ************* ** ** ** ******

VERSION 3.13.2

COMPILED WITH GROMOS-AMBER QM/MM SUPPORT

COPYRIGHTIBM RESEARCH DIVISION

MPI FESTKOERPERFORSCHUNG STUTTGART

The CPMD consortiumHome Page: http://www.cpmd.org

Mailing List: [email protected]: [email protected]

*** Jan 12 2010 -- 16:03:39 ***

Then, we find some technical information about the environment (machine, user,directory, input file, process id) where this job was run:

THE INPUT FILE IS: opt_geo.inpTHIS JOB RUNS ON: iff105c19THE CURRENT DIRECTORY IS:/local/GRS/Users/Tutorials/ACETONE/2-CPMDTHE TEMPORARY DIRECTORY IS:/local/GRS/Users/Tutorials/ACETONE/2-CPMD

O If this is the only input, the program assumes that LMAX is thel for the local potential. You can use another local function by specifying ``LOC= ''. In addition it is possible to assign the local potential to a further potential with ``SKIP= ''.


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THE PROCESS ID IS: 28735

Next are the contents of the &INFO section copied to the output:

******************************************************************************* INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO ******************************************************************************** Acetone molecule ** Geometry optimization *******************************************************************************

Next section contain a summary of some of the parameters read in from the &CPMDsection, or their respective default settings; for example the convergence threshold forwavefunction optimization (set manually) or the maximum number of iterations(default):

OPTIMIZATION OF IONIC POSITIONS

PATH TO THE RESTART FILES: ./GRAM-SCHMIDT ORTHOGONALIZATIONMAXIMUM NUMBER OF STEPS: 10000 STEPSMAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPSPRINT INTERMEDIATE RESULTS EVERY 10001 STEPSSTORE INTERMEDIATE RESULTS EVERY 10001 STEPSSTORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPSNUMBER OF DISTINCT RESTART FILES: 1TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIORFICTITIOUS ELECTRON MASS: 400.0000TIME STEP FOR ELECTRONS: 5.0000TIME STEP FOR IONS: 5.0000CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-06WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIISTHRESHOLD FOR THE WF-HESSIAN IS 0.5000MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10STEPS UNTIL DIIS RESET ON POOR PROGRESS: 10FULL ELECTRONIC GRADIENT IS USEDCONVERGENCE CRITERIA FOR GEOMETRY OPTIMIZATION: 3.000000E-04GEOMETRY OPTIMIZATION BY GDIIS/BFGS

SIZE OF GDIIS MATRIX: 5GEOMETRY OPTIMIZATION IS SAVED ON FILE GEO_OPT.xyzEMPIRICAL INITIAL HESSIAN (DISCO PARAMETRISATION)SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS

NUMBER OF SPLINE POINTS: 5000

The exchange correlation functionals are reported in the lines coming immediatelyafter:

EXCHANGE CORRELATION FUNCTIONALSLDA EXCHANGE: SLATER (ALPHA = 0.66667)LDA CORRELATION: LEE, YANG & PARR

[C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)]GRADIENT CORRECTED FUNCTIONALDENSITY THRESHOLD: 1.00000E-08EXCHANGE ENERGY

[A.D. BECKE, PHYS. REV. A 38, 3098 (1988)]PARAMETER BETA: 0.004200

CORRELATION ENERGY[LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)]

At this point of the output you find which and how many atoms (and their coordinatesin a.u.), electrons and states (we are doing a closed shell calculation, so there are only

doubly occupied states) are in the system, and what pseudopotentials were used withwhich settings:


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*** DETSP| SIZE OF THE PROGRAM IS 3700/ 119392 kBYTES ***

***************************** ATOMS ****************************NR TYPE X(bohr) Y(bohr) Z(bohr) MBL1 C 0.000000 0.000000 0.000000 32 C 2.583394 0.000000 -0.913367 33 C -1.291698 -2.237285 -0.913367 34 O 0.000000 0.000000 2.305466 35 H 2.583394 0.000000 -2.971279 36 H 3.553503 1.680278 -0.227396 37 H 3.553503 -1.680278 -0.227396 38 H -1.291698 -2.237285 -2.971279 39 H -0.321588 -3.917563 -0.227396 3

10 H -3.231915 -2.237285 -0.227396 3****************************************************************

NUMBER OF STATES: 12NUMBER OF ELECTRONS: 24.00000CHARGE: 0.00000ELECTRON TEMPERATURE(KELVIN): 0.00000

OCCUPATION2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0

============================================================| Pseudopotential Report Tue Jan 14 09:55:25 1997 |------------------------------------------------------------| Atomic Symbol : C || Atomic Number : 6 || Number of core states : 1 || Number of valence states : 2 || Exchange-Correlation Functional : || Slater exchange : .6667 || LDA correlation : Lee-Yang-Parr || Exchange GC : Becke (1988) || Correlation GC : Lee-Yang-Parr || Electron Configuration : N L Occupation || 1 S 2.0000 || 2 S 2.0000 || 2 P 2.0000 || Full Potential Total Energy -37.702121 |

| Trouiller-Martins normconserving PP || n l rc energy || 2 S 1.2300 -.49630 || 2 P 1.2300 -.19186 || 3 D .7159 -.19186 || Number of Mesh Points : 615 || Pseudoatom Total Energy -5.370516 |============================================================

============================================================| Pseudopotential Report Thu Nov 30 13:19:26 1995 |------------------------------------------------------------| Atomic Symbol : O || Atomic Number : 8 || Number of core states : 1 || Number of valence states : 2 || Exchange-Correlation Functional : |

| Slater exchange : .6667 || LDA correlation : Lee-Yang-Parr || Exchange GC : Becke (1988) || Correlation GC : Lee-Yang-Parr || Electron Configuration : N L Occupation || 1 S 2.0000 || 2 S 2.0000 || 2 P 4.0000 || Full Potential Total Energy -75.023693 || Trouiller-Martins normconserving PP || n l rc energy || 2 S 1.0500 -.87404 || 2 P 1.0500 -.33186 || 3 D 1.0500 -.33186 || Number of Mesh Points : 631 || Pseudoatom Total Energy -15.775323 |============================================================

============================================================| Pseudopotential Report Thu Nov 30 13:17:19 1995 |


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------------------------------------------------------------| Atomic Symbol : H || Atomic Number : 1 || Number of core states : 0 || Number of valence states : 1 || Exchange-Correlation Functional : || Slater exchange : .6667 || LDA correlation : Lee-Yang-Parr |

| Exchange GC : Becke (1988) || Correlation GC : Lee-Yang-Parr || Electron Configuration : N L Occupation || 1 S 1.0000 || Full Potential Total Energy -.462611 || Trouiller-Martins normconserving PP || n l rc energy || 1 S .5000 -.24002 || 2 P .5000 -.24002 || Number of Mesh Points : 511 || Pseudoatom Total Energy -.462591 |============================================================

***************************************************************** ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL ** C 12.0112 1.2000 NO KLEINMAN S NONLOCAL ** P NONLOCAL ** D LOCAL ** O 15.9994 1.2000 NO KLEINMAN S NONLOCAL ** P NONLOCAL ** D LOCAL ** H 1.0080 1.2000 NO KLEINMAN S NONLOCAL ** P LOCAL *****************************************************************

Then, a section about how the calculation is distributed through the 8 cores: here youcan understand if something wrong happened and you run for example only a serial job:

PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARANCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES0 4333 34682 13 246 976 1 11 4335 34684 14 246 976 2 12 4336 34639 13 243 975 1 13 4336 34676 14 244 976 2 14 4334 34682 13 244 976 1 15 4332 34670 14 244 976 2 16 4338 34676 13 244 976 1 17 4342 34680 14 244 976 2 1

G=0 COMPONENT ON PROCESSOR : 2PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA

*** LOADPA| SIZE OF THE PROGRAM IS 10260/ 120760 kBYTES ***

OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENNUMBER OF CPUS PER TASK 1

OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN*** RGGEN| SIZE OF THE PROGRAM IS 11492/ 121976 kBYTES ***

The following part of the output we see a summary of the settings read in from the&SYSTEM section of the input file or their corresponding defaults and some derived parameters (density cutoff, number of plane waves):

************************** SUPERCELL ***************************SYMMETRY: ORTHORHOMBICLATTICE CONSTANT(a.u.): 20.03110CELL DIMENSION: 20.0311 0.9434 0.9245 0.0000 0.0000 0.0000VOLUME(OMEGA IN BOHR^3): 7010.16987LATTICE VECTOR A1(BOHR): 20.0311 0.0000 0.0000

LATTICE VECTOR A2(BOHR): 0.0000 18.8973 0.0000LATTICE VECTOR A3(BOHR): 0.0000 0.0000 18.5193RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0499 0.0000 0.0000


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RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0529 0.0000RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0540REAL SPACE MESH: 108 108 100WAVEFUNCTION CUTOFF(RYDBERG): 70.00000DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 34686NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 277389****************************************************************

Here we see how CPMD generates the initial guess for the wavefunctionoptimization. In this case it uses a superposition of atomic wavefunctions using an(internal) minimal Slater basis:

*** RINFORCE| SIZE OF THE PROGRAM IS 16052/ 127264 kBYTES ****** FFTPRP| SIZE OF THE PROGRAM IS 19764/ 128656 kBYTES ***

GENERATE ATOMIC BASIS SETC SLATER ORBITALS

2S ALPHA= 1.6083 OCCUPATION= 2.002P ALPHA= 1.5679 OCCUPATION= 2.00

O SLATER ORBITALS2S ALPHA= 2.2458 OCCUPATION= 2.002P ALPHA= 2.2266 OCCUPATION= 4.00

H SLATER ORBITALS1S ALPHA= 1.0000 OCCUPATION= 1.00

INITIALIZATION TIME: 0.39 SECONDS

*** GMOPTS| SIZE OF THE PROGRAM IS 24656/ 141780 kBYTES ****** PHFAC| SIZE OF THE PROGRAM IS 24764/ 152468 kBYTES ****** ATOMWF| SIZE OF THE PROGRAM IS 25784/ 154300 kBYTES ***ATRHO| CHARGE(R-SPACE): 24.000000 (G-SPACE): 24.000000

***************************************************************** ATOMIC COORDINATES *****************************************************************

1 C 0.000000 0.000000 0.0000002 C 2.583394 0.000000 -0.9133673 C -1.291698 -2.237285 -0.9133674 O 0.000000 0.000000 2.3054665 H 2.583394 0.000000 -2.9712796 H 3.553503 1.680278 -0.2273967 H 3.553503 -1.680278 -0.2273968 H -1.291698 -2.237285 -2.9712799 H -0.321588 -3.917563 -0.227396

10 H -3.231915 -2.237285 -0.227396****************************************************************

From the following statement in the output you can see that the Hessian has beeninitialized from a simple guess assuming a molecule with some specified bonds. This behavior can be controlled with the keyword HESSIAN. For bulk systems orcomplicated molecules, it may be better to start from a unit Hessian instead:

INITIALIZE EMPIRICAL HESSIAN>

2 1 3 1 4 1 5 2 6 27 2 8 3 9 3 10 3

>5 1 5 3 6 1 6 4 7 17 3 7 4 8 1 8 2 9 19 2 9 4 10 1 10 4

TOTAL NUMBER OF MOLECULAR STRUCTURES: 1

***************************************************************** ATOMIC COORDINATES *****************************************************************

1 C 0.000000 0.000000 0.0000002 C 2.583394 0.000000 -0.9133673 C -1.291698 -2.237285 -0.9133674 O 0.000000 0.000000 2.3054665 H 2.583394 0.000000 -2.971279


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6 H 3.553503 1.680278 -0.2273967 H 3.553503 -1.680278 -0.2273968 H -1.291698 -2.237285 -2.9712799 H -0.321588 -3.917563 -0.227396

10 H -3.231915 -2.237285 -0.227396****************************************************************

Now the program is ready to start the geometry optimization. You can follow the progress of the optimization in the output file:

CPU TIME FOR INITIALIZATION 0.81 SECONDS

================================================================= GEOMETRY OPTIMIZATION =================================================================NFI GEMAX CNORM ETOT DETOT TCPUEWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS

1 3.015E-02 4.345E-03 -35.648938 -3.565E+01 0.512 1.889E-02 1.442E-03 -36.307687 -6.587E-01 0.463 1.904E-02 7.725E-04 -36.379166 -7.148E-02 0.46

26 1.294E-06 1.055E-07 -36.415776 -2.343E-09 0.4827 9.933E-07 7.580E-08 -36.415776 -1.233E-09 0.48

RESTART INFORMATION WRITTEN ON FILE ./RESTART.1

ATOM COORDINATES GRADIENTS (-FORCES)1 C 0.0000 0.0000 0.0000 -4.443E-02 7.697E-02 -5.004E-022 C 2.5834 0.0000 -0.9134 -3.769E-02 -4.835E-02 4.876E-023 C -1.2917 -2.2373 -0.9134 6.088E-02 8.661E-03 4.903E-024 O 0.0000 0.0000 2.3055 3.158E-02 -5.469E-02 -6.270E-025 H 2.5834 0.0000 -2.9713 -1.090E-02 -5.915E-05 8.858E-036 H 3.5535 1.6803 -0.2274 -9.255E-03 -3.027E-03 -2.712E-047 H 3.5535 -1.6803 -0.2274 6.917E-04 3.287E-03 -1.830E-038 H -1.2917 -2.2373 -2.9713 5.515E-03 9.402E-03 8.862E-039 H -0.3216 -3.9176 -0.2274 -3.189E-03 1.061E-03 -1.824E-03

10 H -3.2319 -2.2373 -0.2274 7.229E-03 6.496E-03 -2.472E-04FILE GEO_OPT.xyz EXISTS, NEW DATA WILL BE APPENDED******************************************************************* TOTAL STEP NR. 27 GEOMETRY STEP NR. 1 ****** GNMAX= 7.696852E-02 ETOT= -36.415776 ****** GNORM= 3.227866E-02 DETOT= 0.000E+00 ****** CNSTR= 0.000000E+00 TCPU= 12.89 *******************************************************************

1 2.130E-02 5.311E-03 -35.580799 8.350E-01 0.462 1.574E-02 1.566E-03 -36.324351 -7.436E-01 0.463 5.503E-03 8.729E-04 -36.400043 -7.569E-02 0.46

...

A geometry optimization is not much else than repeated wavefunction optimizations,where the positions of the atoms are updated according to the forces acting on them.In the first part above you can see, the wavefunction optimization. The columns havethe following meaning:

NFI step number (number of finite iterations) GEMAX largest off-diagonal component CNORM average of the off-diagonal components ETOT total energy DETOT change in total energy TCPU time used for this step

One can see that the calculation stops after the convergence criterion of 1.0d-6 has been reached for the GEMAX value.After printing the positions and forces of the atoms you see a small report block andthen another wavefunction optimization starts. The numbers for GNMAX, GNORM,


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and CNSTR stand for the largest absolute component of the force on any atom,average force on the atoms, and the largest absolute component of a constraint forceon the atoms respectively. They allow you to monitor the progress of the convergenceof the geometry optimization.

Finally, at the end of the geometry optimization, you can see that the forces and thetotal energy have decreased from their initial values as it is to be expected:

******************************************************************* TOTAL STEP NR. 3737 GEOMETRY STEP NR. 214 ****** GNMAX= 2.827646E-04 [3.64E-02] ETOT= -36.489908 ****** GNORM= 1.395703E-04 DETOT= -1.769E-05 ****** CNSTR= 0.000000E+00 TCPU= 9.63 *******************************************************************================================================================= END OF GEOMETRY OPTIMIZATION =================================================================

and we have the final summary of the results; the atom coordinates and a breakdownof the total energy into the various components:

RESTART INFORMATION WRITTEN ON FILE ./RESTART.1

***************************************************************** ** FINAL RESULTS ** *****************************************************************

ATOM COORDINATES GRADIENTS (-FORCES)1 C 0.3033 -0.3710 0.4996 2.238E-04 -3.750E-05 -1.867E-042 C 2.8157 0.1207 -0.8206 -2.828E-04 1.186E-04 1.534E-043 C -1.4005 -2.3884 -0.6592 -1.866E-05 -5.129E-05 1.748E-044 O -0.3055 0.7755 2.4178 1.488E-05 -9.553E-05 2.593E-045 H 2.5171 0.5750 -2.8280 7.045E-06 -1.029E-04 -2.289E-046 H 3.8187 1.6721 0.1124 -6.949E-05 1.507E-04 -3.226E-057 H 3.9948 -1.5943 -0.7676 1.188E-04 -1.722E-05 1.350E-048 H -1.5584 -2.1576 -2.7186 1.045E-05 -8.026E-05 -1.718E-049 H -0.5710 -4.2692 -0.3267 -5.208E-05 -4.544E-05 5.413E-05

10 H -3.2775 -2.3193 0.2103 -1.609E-04 1.615E-04 -2.245E-04

****************************************************************

ELECTRONIC GRADIENT:MAX. COMPONENT = 8.03517E-07 NORM = 6.81662E-08

NUCLEAR GRADIENT:MAX. COMPONENT = 2.82765E-04 NORM = 1.39570E-04

TOTAL INTEGRATED ELECTRONIC DENSITYIN G-SPACE = 24.000000IN R-SPACE = 24.000000

(K+E1+L+N+X) TOTAL ENERGY = -36.48990756 A.U.(K) KINETIC ENERGY = 27.70023623 A.U.(E1=A-S+R) ELECTROSTATIC ENERGY = -27.60801450 A.U.(S) ESELF = 29.92067103 A.U.(R) ESR = 1.71581582 A.U.(L) LOCAL PSEUDOPOTENTIAL ENERGY = -27.66180959 A.U.(N) N-L PSEUDOPOTENTIAL ENERGY = 1.82151808 A.U.(X) EXCHANGE-CORRELATION ENERGY = -10.74183777 A.U.

GRADIENT CORRECTION ENERGY = -0.58344734 A.U.

****************************************************************

The last section of the output reports the memory allocation and the timing of the run:

================================================================


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BIG MEMORY ALLOCATIONSSCR 785159 CATOM 190652PME 520040 PSI 330270YF 330270 GNL 240960ATWFR 301200 SCR 785149XF 330270 RHOE 165135----------------------------------------------------------------[PEAK NUMBER 99] PEAK MEMORY 4872541 = 39.0 MBytes

================================================================

***************************************************************** ** TIMING ** *****************************************************************SUBROUTINE CALLS CPU TIME ELAPSED TIME

INVFFTN 44858 3172.00 323.62FFT-G/S 269168 2733.40 274.36

FWFFT 18690 1730.00 175.40I NVFFT 14953 1726.20 173.92

GCENER 3738 1265.70 128.33FWFFTN 22436 1242.70 125.49FFTCOM 33643 817.30 127.30

VPSI 3747 593.00 58.45GRADEN 3738 460.30 47.00RHOOFR 3737 448.90 45.11

N-FFTCOM 67294 389.10 84.91ODIIS 3737 381.20 38.66

XCENER 3738 353.30 35.86FNONLOC 3747 233.70 23.72

PHASE 33643 219.10 22.22VOFRHOA 3738 172.50 17.50VOFRHOB 3738 131.30 12.75

EICALC 3738 94.90 9.90RNLSM1 3747 66.90 6.84

RGS 3950 38.60 3.57RNLSM2 664 35.50 3.48

----------------------------------------------------------------TOTAL TIME 16305.60 1738.41****************************************************************

CPU TIME : 4 HOURS 33 MINUTES 47.00 SECONDSELAPSED TIME : 0 HOURS 30 MINUTES 10.50 SECONDS

*** CPMD| SIZE OF THE PROGRAM IS 41068/ 152348 kBYTES ***

PROGRAM CPMD ENDED AT: Tue Jun 1 20:03:09 2010

================================================================= COMMUNICATION TASK AVERAGE MESSAGE LENGTH NUMBER OF CALLS == SEND/RECEIVE 43407. BYTES 36127. == BROADCAST 321. BYTES 15557. == GLOBAL SUMMATION 360. BYTES 79725. == GLOBAL MULTIPLICATION 0. BYTES 1. == ALL TO ALL COMM 876851. BYTES 100937. == PERFORMANCE TOTAL TIME == SEND/RECEIVE 5675.900 MB/S 0.276 SEC == BROADCAST 94.488 MB/S 0.053 SEC == GLOBAL SUMMATION 8.258 MB/S 10.435 SEC == GLOBAL MULTIPLICATION 0.000 MB/S 0.001 SEC == ALL TO ALL COMM 417.428 MB/S 212.029 SEC == SYNCHRONISATION 0.025 SEC =================================================================

If you look in your directory, you will see the following files:

Name Content

GEOMETRY Final ionic positions and velocities (in a.u.)GEOMETRY.xyz Final ionic positions and velocities in xyz format

GEO_OPT.xyz All the ionic positions along the geometry optimizationHESSIAN Approximate Hessian used in geometry optimization


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LATEST Info on the last restart file: filename and # times writtenRESTART.1 Restart binary file from which it is possible restart a new

calculation

Now we want to calculate the dipole of the acetone in the zero temperatureoptimized structure just found by using the RESTART.1 file to retrieve theinformation. We can do that modifying the input file this way (seedipole.inp file):&CPMDPROPERTIESRESTART WAVEFUNCTION COORDINATES LATEST&END

&PROPDIPOLE MOMENT&END

PROPERTIES keyword tells CPMD to look at the section &PROP where it isspecifies which properties it has to calculate.

RESTART keyword tells CPMD to read WAVEFUNCTION AND COORDINATESfrom the restart file written in the LATEST file (which was generated in the previouscalculation).

The rest of the input file is the same of the previous one: the coordinates will be notread (since are taken from the restart file) but some number as to put anyway to avoidthe program stops writing some error!

Run the job (single line):

mpirun -np 8 cpmd.x dipole.inp/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP > dipole.out &

In the output file you can see that the following new section:

CALCULATE DIPOLE MOMENT

***************************************************************** PROPERTY CALCULATIONS *****************************************************************

RV30| WARNING! NO WAVEFUNCTION VELOCITIES

RESTART INFORMATION READ ON FILE ./RESTART.1*** PHFAC| SIZE OF THE PROGRAM IS 26772/ 142336 kBYTES ***

CENTER OF INTEGRATION (CORE CHARGE): 0.37726 -0.65932 0.02482

DIPOLE MOMENTX Y Z TOTAL

0.35426 -0.61017 -0.98996 1.21566 atomic units0.90044 -1.55090 -2.51623 3.08990 Debye


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3 The electrostatic grid

The next will be to create a box with an acetone molecule and several watermolecules. We will use for that the xleap program belonging to the Amber106 molecular dynamics package. This package has been devised to deal with biologicalsystems (aminoacids, nucleic acids, etc) and so our acetone has not recognized by it.This is also the case when we want to study somedrug which interacts withtraditional biological systems.In particular, xleap do not know how to assign the partial charges to each atom ofacetone. To do that we will use a standard procedure which has been directlysuggested by the developers of the Amber force fields and which they use to tune that parameters which is not possible to determine experimentally. The procedure is basedon calculating at quantum level the electrostatic potential on a grid around themolecule and then to determine the so-called RESP charges to assign at each atom inorder to reproduce the electrostatic field.

According the recipe of Amber developers we will use the Gaussian09 package7

tocalculate the electrostatic grid by using the 6-31G(d,p) localized basis set and B3LYPexchange correlation functional.First, we need to optimize the geometry again: the level of theory are different and in principle the optimized structures could be different! Here it is the input fileopt_geom.com for Gaussian:%NProcShared=8%chk=./opt_geom.chk%mem=600MB#p opt b3lyp/6-31G(d,p) nosymm iop(6/7=3) gfinput

Acetone geometry optimization

0 1C 0.000000 0.000000 0.000000O 0.000000 0.000000 1.220000C 1.367073 0.000000 -0.483333C -0.683537 -1.183920 -0.483333H 1.367073 0.000000 -1.572333H 1.880433 0.889165 -0.120333H 1.880433 -0.889165 -0.120333H -0.683537 -1.183920 -1.572333H -0.170177 -2.073085 -0.120333H -1.710256 -1.183920 -0.120333

Note: Remember to leave to blank line at the end of the file.

Run the optimization:1. Initialize the environment:

source /home/ippoliti/PROGRAMS/modules/gaussian.sh

2. Run Gaussian:

g09 opt_geom.com &> /dev/null &

P U2/ *80 9-03 $#4 +80/81 8$ $#4 (4, 833.4>>& #$$%&''8+,4.+3)2.7'32*"Z'Y W8/>>-80ZK 201-04 +80/81& #$$%&''((()78/>>-80)*2+'7[$4*#'7[/.'7ZK#41%)#$+


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3. After about one minute the job will end and you can check that theoptimization has been successfully this way:

grep -A 1 Maximum opt_geom.log

Use Molden to retrieve the coordinates of the last optimized configuration:

molden opt_geom.log &

in the Molden Control panel press the Geom. conv. button and the GeomConvergence windows will appear. In that window you can select any step of theoptimization procedure; to save the optimized geometry, select the last one andwrite (save) the structure (in xyz format).

Now, use Gaussian again to calculate the electrostatic grid by theelectrostatic_grid.com input file:First, make a copy of the checkpoint file from the optimization run:cp opt_geom.chk electrostatic_grid.chk

%NProcShared=8%chk=./electrostatic_grid.chk%mem=600MB#p b3lyp/6-31G(d,p) nosymm iop(6/33=2) pop(chelpg,regular) guess=read gfinput geom.=check

Acetone electrostatic grid calculation

0 1

(put a blank line at the end)

The wave function (guess=read) as well as the final (optimized) coordinates(geom=check) are read from the checkpoint file. The electrostatic grid will be written inthe log file: look for the string ESP fit Center.

4 Partial charges

The program Antechamber inside the Amber10 package is able to read the electrostaticgrid in a log file of Gaussian and calculate the RESP charges associated to the atoms ofyour molecule. To use Antechamber and every other program of the Amber10 suite, we

firstly need to initialize the environment:source /home/ippoliti/PROGRAMS/modules/amber.sh

Copy the log file of Gaussian with the electrostatic grid information on a new directoryand use the following command:8

antechamber -i electrostatic_grid.log -fi gout -c resp -nc 0 -m 1 -oacetone.resp.prep -fo prepi -rn ACET

L V/0 >-+%1J $#4 *2++803 \80$4*#8+,4.] $2 #8X4 8 >#2.$ 34>*.-%$-20 29 $#4 +480-07 29 811 $#42%$-20 .4*270-?43 ,J 80$4*#8+,4.)


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Actually, Antechamber recalls several programs in sequence which produce manydifferent intermediate files in your directory. When the process ends correctly youshould see the fileacetone.resp.prep which is the file with the partial RESP chargesthat we will use in the next step (copy it in a new directory and move to it).

5 Water box

It is time to create the water box containing the acetone and the files necessary to run ashort classical Molecular Dynamics (MD) run. In fact, we want then to perform aclassical pre-equilibration of the system, in order to relax it near to a stable state.9 For this aim we will use the Graphical User Interface Xleap of Amber10:

xleap -f /home/ippoliti/PROGRAMS/src/amber11/dat/leap/cmd/leaprc.ff99SB &

where the file leaprc.ff99SB is used to load all libraries which contains the parameters ofthe Amber force field 99SB. Such a force field like any others has been tuned todescribe aminoacids, nucleic acids, etc but there is no information about acetone. Forthis reason we have calculated the partial charges, which now we can load in Xleap bytyping the following command (in the Xleap main window):10

loadamberprep acetone.resp.prep

and for the same reason some other parameters are still missing and have to be addedmanually. Most of them can be retrieved by the general Amber force field for organicmolecules GAFF:

loadamberparams /home/ippoliti/PROGRAMS/src/amber11/dat/leap/parm/gaff.dat

other ones, however, have to provide manually. It is not difficult to calculate them buthere we will no explain how to do11. We have already prepared a file with such missing parameters (above all bond and angles ones) and they can be load in Xleap by thefollowing command:

loadamberparams /work/Tutorial/ACETONE/5-XLEAP/acetone.frcmod

You can now give a look at your system by the command edit:

edit ACET

You can also check if all the parameters for the acetone have been loaded:

check ACET

Finally, you can save the topology and coordinates files for your ACET unit by typing:

K V4+4+,4. $#4 $-+4 >$4% 92. 8 *18>>-*81 ;D ./0 -> ^%>H (#-14 $#4 $-+4 >$4% 92. 8 _/80$/+ ;D ->^9>) `2H $#4 *18>>-*81 %.4Q4_/-1-,.8$-20 -> 4>>40$-81 >-0*4 $J%-*81 .418a8$-20 $-+4> 8.4 29 $#4 2.34.29 "Z>Q"ZZ> 29 %>b"Z J0$8a 92. 80J c148% *2++803 *80 ,4 .4*811 ,J $J%-07 $#4 *2++803 (-$#2/$ 80J8.7/+40$>)"" V494. $2 $#4 6+,4. +80/81H 92. 4a8+%14)


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saveamberparm ACET acetone.top acetone.rst

However, we want to study the acetone in water and therefore we need to solvate thesystem, before:

solvatebox ACET TIP3PBOX 14

TIP3PBOX specifies that we solvate with the classical water model moleculeTIP3P12; an orthorhombic box whose walls are at least 14 from any acetones atomshas been created:

edit ACET

From the new window you can also look at the partial charges and other parameters ofyour system:

Select the atoms Edit/Edit selected atoms

Finally, we save the topology and coordinates files for our solvated system:

saveamberparm ACET acetone_solv.top acetone_solv.rst

Copy the two files to another folder.By the VMD software13 you can visualize your system:

vmd parm7 acetone_solv.top rst7 acetone_solv.rst

6 Pre Equilibration

We need now to equilibrate the system at force field level in order to later start theQM/MM simulation from a configuration not so far from an equilibrium one (at theQM/MM level).To run MD simulation we will use the sander program of the AMBER10 package.We proceed this way:14

1. First, classical minimization of the system restraining the acetone molecule tothe initial position: this step is performed since the initial Xleap solvation is not physically reasonable (no hydrogen bonds, etc) and this way we favour water

2. molecules to orient correctly around the acetone:

mpirun -np 8 sander.MPI -O -i 1-restraint.inp -o eq_restraint.out -c acetone_solv.rst \-p acetone_solv.top -r eq_restraint.rst -ref acetone_solv.rst -inf eq_restraint.info &

"5 #$$%&''40)(-G-%43-8)2.7'(-G-'T8$4.[+2341"A d;D e>4.f> W/-34& #$$%&''((()G>)/-/*)43/'V4>48.*#'X+3'*/..40$'/7'"E 611 $#4 -0%/$ 9-14 92. >8034. *80 ,4 92/03 -0 $#4 92134.&

'(2.G'


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Note: the command tail eq_restraint.info can be used to monitor theminimization and verify that it does not reach the max number of steps but stop beforesatisfying the convergence criteria.

3. Then, a not constrained minimization is performed(single line command) :

mpirun -np 8 sander.MPI -O -i 2-minimization.inp -o eq_minimization.out -ceq_restraint.rst -p acetone_solv.top -r eq_minimization.rst -infeq_minimization.info &

4. Now, we take the system at 300 K with MD at constant volume and a linearheating. In this step we constrainweakly acetone to the initial position so thatwater can spread all around the acetone without forming holes. Since the liquidwater relaxation time is order of 10 ps we need to perform a > 10 ps MD:

mpirun -np 8 sander.MPI -O -i 3-heating.inp -p acetone_solv.top -ceq_minimization.rst -ref eq_minimization.rst -o eq_heating.out -r eq_heating.rst -xeq_heating.crd -e eq_heating.en -inf eq_heating.info &

5. Finally, we couple our system simultaneously to a thermostat at 300 K and a barostat at 1 atm and perform an NPT simulation to let the density of the systemto reach the equilibrium value at room condition (~ 1g/cm3 since the most isformed by water):

mpirun -np 8 sander.MPI -O -i 4-eq_density.inp -p acetone_solv.top -ceq_heating.rst -o eq_density.out -r eq_density.rst -x eq_density.crd -eeq_density.en -inf eq_density.info &

Note: when the last step has ended, you can fast analyze the behavior of all the physically relevant quantities of your system (like the density for example) by usingthe perl script process_mdout.perl

(The perl-script is located in the sample subfolder 6-SANDER/analysis)

Box Density

mkdir analysiscd analysisprocess_mdout.perl ../eq_density.outxmgrace summary.DENSITY

Why is density smaller than 1g/cm3?

VMD visualization:

Final coordinates: vmd parm7 acetone_solv.top rst7 outputfile.rstTrajectory: vmd parm7 acetone_solv.top crdbox outputfile.crd


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"K

7 Reimaging

Lets give a look at the last configuration you obtained from the classical moleculardynamics equilibration:

cd ..vmd -parm7 acetone_solv.top -rst7 eq_density.rst

What did happen to our orthorhombic box?

The image shows your system without applying the periodic boundary conditions(PBC) that sander and all the other programs of Amber10 use. So, molecules driftover time and may span multiple periodic cells; this is normal when you are working

on Amber10 or on some other molecular dynamics package. However, now we wantto move to CPMD in order to perform a QM/MM MD simulation, and CPMD doesnot apply automatically PBC. Consequently, we need to reimage the coordinatesinto the primary unit cell. We can use the ptraj program15 of the Amber10 suite toaccomplish this task. Move the topology and coordinates files to another folder andthen create the input fileeq_density.ptraj for ptraj:

trajin eq_density.rst ! coordinates file to read trajout eq_density_reimaged.rst restart ! output file in the same format as the inputcenter :1 ! center the box to the geometric center of residue 1 image center ! force all the molecules into the primary unit cell

Run ptraj according this syntax:

ptraj acetone_solv.top < eq_density.ptraj

Verify that the imaging has been correctly done:

vmd -parm7 acetone_solv.top -rst7 eq_density_reimaged.rst.1

"O #$$%&''8+,4.+3)2.7'32*"Z'6+,4.)%39


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8 Convert MD files

Copy the topology and the reimaged coordinates files to a new directory and typingthe following command:

Conv_7.x acetone_solv.top eq_density_reimaged.rst.1 solvate

Conv_7.x is an in-house program written to convert the Amber MD files in theGROMOS format. This because the QM/MM interface of CPMD works with such aformat. The option solvate let us specify that the water molecules should be treatedas solvent ones: this is useful only if you are interested to read in the log files ofCPMD energies and other quantities partitioned in solute and solvent components.

The converter will produce 5 files: gromos.top the Gromos topology file for our system gromos.inp the Gromos input file gromos.g96 the coordinates file in g96 format gromacs.top the Gromacs topology file ffgro96.itp the itp file for the Gromacs software

We need only the first 3 files, but some changes16 have to be done in order tocorrectly set up a QM/MM MD simulation:

Changes in gromos.inp

1 - In the section SYSTEM the two numbers should be in sequence:

Number of (identical) solute (not necessarily the QM part!) molecules Number of (identical) solvent (not necessarily the MM part!) molecules

Such information can be retrieved, for example, by typing on the promptcommand line:

tail gromacs.top

"P >44 81>2 #$$%&''((()*%+3)2.7'+80/81'02345PY)#$+1


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2 - In the section BOUNDARY:

The first number should be 0 for isolated system; >0 if PBC in parallelepiped box has been used;


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9 QM/MM MD

Copy the modified files and the gromos.g96 file to a new directory.

At this point, we have all the files which describe the MM part and its interactions;the last step will be to write the input file for CPMD with the instructions for thesimulation and the definition of the QM part. A CPMD input file for a QM/MMsimulation is similar to the CPMD input file for a standard QM calculation which has been described in paragraph 2 (section &INFO, &CPMD, &SYSTEM, &ATOMS,&DFT). However, there are 6 main differences which should always be taken intoaccount when you deal with the QM/MM interface of CPMD:

1. In the &CPMD section the keyword QMMM has to be added.2. A new &QMMM section, which we will explain in detail below, is

mandatory.

3.

The QM atoms are specified in the &ATOMS section similar to normalCPMD calculations. Instead of explicit coordinates one has to provide theatom index as given in the Gromos topology and coordinates files:

vi gromos.g964. The keyword ANGSTROM in the &SYSTEM section cannot be used, so any

length has to be specified in a.u.5. The option ABSOLUTE in the keyword CELL cannot be used. Therefore the

correct syntax for the size of the rectangular box Ax BxC is

A B/A C/A 0 0 0

P) The QM system in a QM/MM calculation can only be dealt as isolated system,i.e. without explicit PBC since there is the MM environment all round it.Even though we are requesting an isolated system calculation (SYMMETRYkeyword with the option ISOLATED SYSTEM or 0), the calculation is, infact, still done in a periodic cell (we are still using plane wave basis set!).Since acetone has a dipole moment, we have to take care of the long rangeinteractions between periodic images and there are methods (activated withthe keyword POISSON SOLVER in the &SYSTEM section) implemented inCPMD to compensate for this effect. We will choose the TUCKERMANPoisson solver 17 since it has been proven to be the most effective one withtypical systems studied in biology. Decoupling of the electrostatic images inthe Poisson solver requires to increase the box size over the dimension of themolecule: practical experience shows that 3.5 space between the outmostatoms and the box is usually sufficient for typical biological systems.

&QMMM section

In this paragraph we will review the most relevant keywords to specify in the&QMMM section of the CPMD input file. See for example18 for a completelist:

"Y G.J. Martyna and M. E. Tuckerman, J. Chem. Phys. 110, 2810 (1999). "L #$$%&''((()*%+3)2.7'+80/81'02345OL)#$+1


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TOPOLOGY: On the next line the name of a Gromos topology filehas to be given.

COORDINATES: On the next line the name of a Gromos96 formatcoordinate file has to be given.

INPUT: On the next line the name of a Gromos input file has to be given.AMBER: An Amber functional form for the classical force fieldis used.

ELECTROSTATICCOUPLING: The electrostatic interaction of the quantum system

with the classical system is explicitly kept into accountfor all classical atoms at a distancer ! RCUT_NNfrom any quantum atom and for all the MM atoms at adistance of RCUT_NN< r ! RCUT_MIX and acharge larger than0.1e (NN atoms). MM-atoms with acharge smaller than 0.1e and a distance of RCUT_NN< r ! RCUT_MIX and all MM-atoms withRCUT_MIX< r ! RCUT_ESP are coupled to theQM system by a ESP coupling Hamiltonian (ECatoms).

If the additional LONG RANGE keyword is specified,the interaction of the QM-system with the rest of theclassical atoms is explicitly kept into account viainteracting with a multipole expansion for the QM-system up to quadrupolar order. A file named

MULTIPOLE is produced.If LONG RANGE is omitted the quantum system iscoupled to the classical atoms not in the NN-area andin the EC-area list via the force-field charges.

If the keyword ELECTROSTATIC COUPLING isomitted, all classical atoms are coupled to the quantumsystem by the force-field charges (mechanicalcoupling): computational expensive calculation!

RCUT_NN: The cutoff distance for atoms in the nearest neighborregion from the QM-system is read from the next line.We will use the default value of 10 a.u.

RCUT_MIX: The cutoff distance for atoms in the intermediateregion is read from the next line. We will use the valueof 15 a.u.

RCUT_EXP: The cutoff distance for atoms in the ESP-area is readfrom the next line. We will use the value of 20 a.u.

UPDATE LIST: On the next line the number of MD steps betweenupdates of the various lists of atoms forELECTROSTATIC COUPLING is given. At every listupdate a file INTERACTING_NEW.pdb is created(and overwritten).


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SAMPLEINTERACTING: The sampling rate for writing a trajectory of the

interacting subsystem is read from the next line. Withthe additional keyword OFF or a sampling rate of 0,those trajectories are not written.

ARRAYSIZES: Parameters for the dimensions of various internal arrayscan be given in this block. The syntax is one label andthe according dimension per line. The suitable parameters can be estimated using the scriptestimate_gromos_size.sh :

estimate_gromos_size.sh gromos_mod.top

This section of the input has to be terminated by a linecontaining END ARRAYSIZES.

Now, we have all the elements to write a CPMD input file for a QM/MM simulation.But which steps do we need to perform a stable Car-Parrinello MD?We have the equilibrated coordinates at room conditions obtained from a classical MD:this is a good starting point, however we still need to equilibrate the system at QM/MMlevel since the two levels of theory are different.

Therefore, as we have done in the second paragraph, we should at first optimize thegeometry of the system. Unfortunately, all the optimizer algorithms in CPMD do notwork together with the QM/MM interface. Consequently, we have to use some trickto find a minimal energy structure (at QM/MM level). In particular in this tutorial wewill perform a simulated annealing (keyword ANNEALING IONS) , i.e. we run a CP-dynamics where and gradually removing kinetic energy from the nuclei by multiplyingvelocities with a factor (in our case it is set to 0.99, so 1% of the kinetic energy will beremoved in every step). Here it is theannealing.inp file which perform this preliminary step:

&QMMMTOPOLOGYgromos_mod.top

COORDINATESgromos.g96

INPUTgromos_mod.inp

ELECTROSTATIC COUPLING LONG RANGE

RCUT_NN10RCUT_MIX15

RCUT_ESP20

UPDATE LIST100

SAMPLE_INTERACTING0

AMBERARRAYSIZES

MAXATT 16MAXAA2 11MAXNRP 20MAXNBT 15MAXBNH 16MAXBON 13MAXTTY 14


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MXQHEH 22MAXTH 13MAXQTY 10MAXHIH 10MAXQHI 10MAXPTY 14MXPHIH 28MAXPHI 11MAXCAG 11MAXAEX 20024MXEX14 22

END ARRAYSIZES&END

&CPMDQMMMMOLECULAR DYNAMICS CPISOLATED MOLECULEQUENCH BOANNEALING IONS0.99

TEMPERATURE300

EMASS600.

TIMESTEP5.0

MAXSTEP10000

TRAJECTORY SAMPLE0

STORE100

RESTFILE1

&END

&SYSTEMPOISSON SOLVER TUCKERMAN

SYMMETRY0CELL18.61 1.11 0.95 0 0 0

CUTOFF70.

CHARGE0.0

&END

&DFTFUNCTIONAL BLYP&END

&ATOMS*H_MT_BLYP.psp KLEINMAN-BYLANDER

LMAX=S64 5 6 8 9 10

*C_MT_BLYP.psp KLEINMAN-BYLANDERLMAX=P3

2 3 7

*O_MT_BLYP.psp KLEINMAN-BYLANDERLMAX=P1

1&END

Some comments on the keywords in the &CPMD section which are not explained, yet:


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MOLECULAR DYNAMICS CP: Perform a molecular dynamics run.CP stands for a Car-Parrinello type of MD.

ISOLATED MOLECULE: Calculate the ionic temperature assuming thatthe system consists of an isolated molecule orcluster.

QUENCH BO: the wavefunction is converged at the beginning of the MD run.TEMPERATURE: The initial temperature for the atoms in Kelvin

is read from the next line: we start from 300 Ksince it is the temperature at which weequilibrate the system classically.

EMASS: The fictitious electron mass in atomic units forthe CP dynamics is read from the next line.We choose 600 a.u. but ideally a careful set oftests should be done to verify that adiabaticityconditions to be met19: this and the followingone are the only parameters to tune in order todecouple the electronic and ionic degrees offreedom and minimize their energy transfer.

TIMESTEP: The time step in atomic units is read from thenext line. We use the default time step of 5 a.u.~ 1.2 fs.

MAXSTEP: The maximum number of steps for moleculardynamics to be performed. The value is readfrom the next line.

TRAJECTORY SAMPLE: Store the atomic positions, velocities andoptionally forces at N every time step on theTRAJECTORY file. N is read from the nextline. If N =0 the trajectory file will not bewritten.

STORE: The RESTART file is updated every N steps. N is read from the next line. Default is at theend of the run.

RESTFILE: The number of distinct RESTART filesgenerated during CPMD runs is read from thenext line. The restart files are written in turn.Default is 1.

Moreover, here it is a simple procedure to obtain the sizes of the box to insert under theCELL keyword by using standard bash commands:

Create a file with the coordinate of the atoms belong to the QM part:

grep CET gromos.g96 > QM.coor

Reorder the lines in the column 5 (6,7) for the coordinate x (y,z) with anincreasing numerical (-n) order:

sort -k 5 -n QM.coor

"K #$$%&''((()$#42*#4+)./#.Q/0-Q,2*#/+)34'.4>48.*#'+8.a'+8.a)%39


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Take the last value (L) of the column (in nm), subtract it to the first (F) one,add 0.7 nm (i.e. 2 * 3.5 for the Poisson solvers requirements) and thenconvert it to a.u.:

echo "(L - F + 0.7)*10/0.529" | bc l

Finally remember that under the CELL keyword of the CPMD input file thesize of the quantum cell will be inserted according to the syntax:

size_x size_y/size_x size_z/size_x 0 0 0

1 - ANNEALING

We are now ready to run the annealing (copy all the file in a folder calledANNEALING):

mpirun -np 8 cpmd.x annealing.inp/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP > annealing.out &

While the simulation proceeds you can monitor the decreasing temperature (thirdcolumn named TEMPP) this way:

tail -f annealing.out

When the temperature reaches about 2-4 K we can softly stop the calculation (thatis in order to make it write a RESTART file) by typing on the prompt line:

touch EXIT

The final configuration will be stored in the RESTART.1 file.More files will be generated during a QM/MM CP simulation:

QMMM_ORDER The first line specifies the total number of atoms (NAT) and thenumber of quantum atoms (NATQ). The subsequent NAT linescontain, for every atom, the gromos atom number, the internalCPMD atom number, the CP species number isp and thenumber in the list of atoms for this species NA(isp). Thequantum atoms are specified in the first NATQ lines.

CRD_INI.g96 Contains the positions of all atoms in the first frame of thesimulation in Gromos extended format (g96).

CRD_FIN.g96 Contains the positions of all atoms in the last frame of thesimulation in Gromos extended format (g96).

INTERACTING.pdb Contains (in a non-standard PDB-like format) all the QM atomsand all the MM atoms in the electrostatic coupling NN list. The5-th column in this file specifies the gromos atom number asdefined in the topology file and in the coordinates file. The 10-th column specifies the CPMD atom number as in the

TRAJECTORY file. The quantum atoms are labeled by theresidue name QUA.


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INTERACTING_NEW.pdb The same as before, but it is created if the fileINTERACTING.pdb is detected in the current workingdirectory of the CPMD run.

MM_CELL_TRANS The QM system (atoms and wavefunction) is always re-centered in the given supercell. T his file contains, thetrajectory of the re-centering offset for the QM-box. The firstcolumn ist the frame number (NFI) followed by the x-, y-, andz-component of the cell-shift vector.

ENERGIES Contains all the energies along the trajectory.

Lets give a closer look at the output file annealing.out which present some newsections:

CAR-PARRINELLO MOLECULAR DYNAMICS

PATH TO THE RESTART FILES: ./ITERATIVE ORTHOGONALIZATION

MAXIT: 30EPS: 1.00E-06

MAXIMUM NUMBER OF STEPS: 10000 STEPSMAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPSPRINT INTERMEDIATE RESULTS EVERY 10001 STEPSSTORE INTERMEDIATE RESULTS EVERY 100 STEPSSTORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPSNUMBER OF DISTINCT RESTART FILES: 1TEMPERATURE IS CALCULATED ASSUMING AN ISOLATED MOLECULE

In CPMD, atoms are frequently referred to as ions, which may be confusing. This isdue to the pseudopotential approach, where you integrate the core electrons into the(pseudo)atom which then could be also described as an ion. See for example thefollowing output segment:

FICTITIOUS ELECTRON MASS: 600.0000TIME STEP FOR ELECTRONS: 5.0000TIME STEP FOR IONS: 5.0000QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACESIMULATED ANNEALING OF IONS WITH ANNERI = 0.990000ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLEDION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED

This part of the output tells us, that the TIMESTEP keyword was recognized as wellas the output option and that there will be no temperature control, i.e. we will do amicrocanonical (NVE-ensemble) simulation.

Then, several sections devoted to describe in detail the QM/MM interface and its dataimmediately follow:

INITIALIZATION TIME: 1.05 SECONDS

*** MDPT| SIZE OF THE PROGRAM IS 95528/ 288728 kBYTES ****** PHFAC| SIZE OF THE PROGRAM IS 97076/ 300980 kBYTES ****** ATOMWF| SIZE OF THE PROGRAM IS 98100/ 302796 kBYTES ***ATRHO| CHARGE(R-SPACE): 24.000000 (G-SPACE): 24.000000

RE-CENTERING QM SYSTEM AT EVERY TIME STEP

BOX TOLERANCE [a.u.] 7.00000000000000

BOX SIZE [a.u.] QM SYSTEM SIZE [a.u.]X DIRECTION: CELLDIM = 18.6100; XMAX-XMIN= 5.3773


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Y DIRECTION: CELLDIM = 20.6571; YMAX-YMIN= 7.3868Z DIRECTION: CELLDIM = 17.6795; ZMAX-ZMIN= 4.3595

>>>>>>>> QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACE


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MEAN VALUE +/- RMS DEVIATION [-^2]**(1/2)

ELECTRON KINETIC ENERGY 0.000867 0.300539E-03IONIC TEMPERATURE 37.2640 52.8318DENSITY FUNCTIONAL ENERGY -56.788301 0.907159CLASSICAL ENERGY -56.369667 1.48329CONSERVED ENERGY -56.368800 1.48357NOSE ENERGY ELECTRONS 0.000000 0.00000

NOSE ENERGY IONS 0.000000 0.00000CONSTRAINTS ENERGY 0.000000 0.00000RESTRAINTS ENERGY 0.000000 0.00000ION DISPLACEMENT 0.306287 0.932230E-01CPU TIME 1.5641

2 TEST

To verify that the reached configuration is physically "reasonable", a good test is torun a simulation in a NVE ensemble and monitoring the temperature (column 3) andthe physical energy (column 5): if after some steps these two quantities stabilize(usually oscillating around a value of temperature smaller than 100 K) then we can beconfident that the RESTART.1 file previously obtained is a good minimal energystructure. On the other hand, if energy and/or temperature continuously increase thatmeans we have not a good structure and another annealing procedure is required bystarting from another point (for example after heating the system at 300 K in order tomove the system away from that wrong energy potential basin). The test can beaccomplished by the following procedure:

Create a new folder:

mkdir TESTcd TEST

Copy the following files from the previous calculation:

cp ../gromos* .cp ../RESTART.1 RESTARTcp ../annealing.inp test.inp

Modify thetest.inp file in order to change the &CPMD section so as toappear:

&CPMDRESTART COORDINATES VELOCITIES WAVEFUNCTIONQMMMMOLECULAR DYNAMICS CPISOLATED MOLECULEEMASS600.TIMESTEP5.0MAXSTEP3000TRAJECTORY SAMPLE0&END


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Note: in the RESTART line there is no LATEST option: this way CPMDexpects to read data from a file named exactly RESTART.

Run the test:

mpirun -np 8 cpmd.x test.inp/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP > test.out &

Monitor the simulation:

tail f test.out

When it ends you can plot on a graph the temperature and the physical energy by gnuplot:

gnuplotp 'ENERGIES' u 1:3 w lp 'ENERGIES' u 1:5 w lquit

3 HEATING

If the test went well, we can come back to the configuration obtained by annealingand start heating the system to room temperature. There are several methodsimplemented in CPMD to do that. We choose to increase the target temperature of athermostat (coupled to the system) linearly at each step by performing a usual CPdynamics. A simple Berendsen-type thermostat20 will be applied.Two more keywords are required in &CPMD section with respect to the previousinput file:

1. TEMPERATURE with the option RAMP; 3 numbers have to be specified onthe line below the keyword: initial and target temperature in K and theramping speed in K per atomic time unit (to get the change per timestep youhave to multiply it with the value of TIMESTEP). Read the initial temperaturefrom the output file of the annealing procedure.

5) BERENDSEN with the option IONS; 2 numbers has to be specified on theline below the keyword: the target temperature (the initial one in our case) andthe time constant ! in a.u. (0.12 ps is a reasonable value).

The procedure to accomplish the heating can be summarized this way:

5Z i) I) B) F4.403>40H I) C) ;) C2>$+8H T) j) X80 W/0>$4.40H 6) D-h218H I) V) i88GI) B#4+) C#J>H L"H APLE M"KLEN)


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Create a new folder:

mkdir HEATINGcd HEATING

Copy the following files from the previous calculation:

cp ../ANNEALING/gromos* .cp ../ANNEALING/RESTART.1 RESTARTcp ../TEST/test.inp heating.inp

Modifyheating.inp: vi heating.inp Include the following lines in the &CPMD section:

BERENDSEN IONS

3.8 1000TEMPERATURE RAMP3.8 340.0 1

Monitor the temperature: tail f heating.out

If the temperature reach approximately the target temperature even before theMAXSTEP number of steps are performed you can stops the simulation:

touch EXIT

4 PRODUCTION RUN

T4 8.4 9-0811J .483J $2 ./0 8 BC +214*/18. 3J08+-*> -0 .22+ *203-$-20>) />/81H (4 (-11 *.48$4 8 04( 92134.&

mkdir PRODUCTION-RUNcd PRODUCTION-RUN

and then we will copy the necessary files there in order to start the calculation fromthe last configuration got from the heating procedure:

cp ../HEATING/gromos* .cp ../HEATING/RESTART.1 RESTARTcp ../HEATING/heating.inp cpmd.inp

To run CP molecular dynamics we need to modify the previous input file:

We want to restart from previous wavefunction, coordinates and velocitiessince we want to conserve the temperature information from the RESTARTfile. Therefore we will preserve the option VELOCITIES in the RESTARTkeyword and we will remove TEMPERATURE keyword.


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We will replace the Berendsen thermostat with the Nose-Hoover chains21: this because the second kind of thermostat preserves the Maxwell distribution ofthe velocities and so it is more physically meaningful. In more technicalwords, it provides an NVT ensemble for a system in equilibrium.The keyword that turns it on is NOSE, and then you have to specify thedegrees of freedom to which you want to apply it (IONS); the targettemperature in Kelvin and the thermostat frequency in cm-1 are read from thenext line:

NOSE IONS300 4000

For the choice of frequency at which the energy transfer happens, you haveonly to pay attention not to select a resonance vibrational frequency of yoursystem.

We will reintroduce the keyword MAXSTEP to perform 10000 steps (or moreif you have time: typical CPMD trajectories nowadays are tens of ps long!)

Finally, we want to save 10 restart files (i.e. configurations from which wewill calculate the dipole moment of acetone) equally separated in time alongthe trajectory. We can do that by properly using the keyword RESTFILE andSTORE:

STORE100RESTFILE10

This way CPMD will create ten restart files in sequence called RESTART.1,RESTART.2, , RESTART.10 each one after 1000 steps of dynamics.

Running meaningful Car-Parrinello dynamics simulation requires adiabaticityconditions to be met, i.e. the separation of the electronic and ionic degrees offreedom.Theoretically such separation can be achieved by separating the power spectrum ofthe orbital classical fields from the phonon spectrum of the ions (the gap between thelowest electronic frequency and the highest ionic frequency should be large enough).

Since the electronic frequencies depend on the fictitious electron mass EMASS oneshould carefully optimize its value and rise the lowest frequency appropriately.The adiabaticity can be observed by running test simulations and looking at theenergy components.In particular, the fictitious kinetic energy of the electronic degrees of freedom(EKINC, second column in the ENERGIES file) might have a tendency to grow.However, after an initial transfer of a little kinetic energy, the electrons should bemuch colder" than the ions, since only then will the electronic structure remain closeto the Born-Oppenheimer surface and thus the wavefunction and forces derived fromit will be meaningful. Therefore, we must always monitor the behavior of the EKINC

5" `) h2>k 803 ;) S) l14-0H ;21) C#J>) OZH "ZOO M"KLANR `) h2>kH ;21) C#J>) O5H 5OO M"KLENR `) h2>kHI) B#4+) C#J>) L"H O"" M"KLENR `) h2>kH C.27) ) `/%%1) "ZAH " M"KK"NR T) W) i22X4.HC#J>) V4X) 6 A"H "PKO M"KLON)


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in order to verify the system keeps being in the adiabatic regime:

TOTAL INTEGRATED ELECTRONIC DENSITYIN G-SPACE = 24.000000IN R-SPACE = 24.000000

(K+E1+L+N+X+Q+M) TOTAL ENERGY = -57.87866446 A.U.(K+E1+L+N+X) TOTAL QM ENERGY = -36.47942711 A.U.(Q) TOTAL QM/MM ENERGY = 0.00000000 A.U.(M) TOTAL MM ENERGY = -21.38112962 A.U.

DIFFERENCE = -0.01810773 A.U.(K) KINETIC ENERGY = 27.71754549 A.U.(E1=A-S+R) ELECTROSTATIC ENERGY = -27.62122216 A.U.(S) ESELF = 29.92067103 A.U.(R) ESR = 1.68558813 A.U.(L) LOCAL PSEUDOPOTENTIAL ENERGY = -29.41090607 A.U.(N) N-L PSEUDOPOTENTIAL ENERGY = 3.57237860 A.U.(X) EXCHANGE-CORRELATION ENERGY = -10.73722297 A.U.

GRADIENT CORRECTION ENERGY = -0.58313547 A.U.

NFI EKINC TEMPP EKS ECLASSIC EHAM EQM DIS TCPU1 0.00001 302.5 -57.87866 -54.48084 -54.48082 -36.47943 0.538E-05 1.502 0.00011 302.3 -57.87721 -54.48093 -54.48082 -36.47936 0.214E-04 1.473 0.00027 302.2 -57.87578 -54.48109 -54.48082 -36.47937 0.480E-04 1.354 0.00037 302.0 -57.87431 -54.48118 -54.48081 -36.47937 0.849E-04 1.505 0.00039 301.9 -57.87280 -54.48119 -54.48080 -36.47937 0.132E-03 1.356 0.00039 301.8 -57.87125 -54.48118 -54.48079 -36.47937 0.190E-03 1.357 0.00037 301.6 -57.86966 -54.48116 -54.48078 -36.47937 0.258E-03 1.678 0.00037 301.5 -57.86803 -54.48115 -54.48078 -36.47936 0.336E-03 1.359 0.00037 301.3 -57.86636 -54.48114 -54.48077 -36.47936 0.425E-03 1.46

NBPML: 80733 ELEMENTS IN THE PAIRLIST

10 0.00037 301.2 -57.86466 -54.48114 -54.48077 -36.47935 0.523E-03 1.3711 0.00036 301.0 -57.86291 -54.48113 -54.48077 -36.47934 0.632E-03 1.4612 0.00035 300.9 -57.86112 -54.48111 -54.48076 -36.47932 0.752E-03 1.3513 0.00035 300.7 -57.85927 -54.48107 -54.48073 -36.47931 0.881E-03 1.3514 0.00034 300.5 -57.85740 -54.48106 -54.48072 -36.47929 0.102E-02 1.4615 0.00033 300.4 -57.85551 -54.48106 -54.48073 -36.47928 0.117E-02 1.3516 0.00032 300.2 -57.85357 -54.48105 -54.48073 -36.47927 0.133E-02 1.4617 0.00031 300.0 -57.85159 -54.48103 -54.48072 -36.47926 0.150E-02 1.3518 0.00030 299.8 -57.84956 -54.48101 -54.48070 -36.47925 0.169E-02 1.5119 0.00030 299.7 -57.84751 -54.48099 -54.48070 -36.47924 0.188E-02 1.42

Ensuring adiabaticity of CP dynamics consists of decoupling the two subsystems and

thus minimizing the energy transfer from ionic degrees of freedom to electronic ones.In this sense the system during CP dynamics simulation should be kept in ametastable state.

*"+, & 80J $-+4 J2/ 02$-*4 >2+4$#-07 >$.8074 M803 4X40 -9 J2/ 32 02$bN m X4.J/>49/1 >/774>$-20 -> 6ST6U` 122G 8$ J2/. >-+/18$-20> ,J >2+4 X->/81-?8$-20 $221&$#4 +2>$ 29 $#4 %.2,14+ 8.4 -++43-8$41J -340$-9-43 8$ 8 7180*4n/81-?4 8 BCQ;; >-+/18$-20 J2/ *80 />4 X+3 55 &

vmd -g96 CRD_INI.g96 -cpmd TRAJECTORY

55 60J *2++803 29 X+3 *80 ,4 81>2 4a4*/$4 ,J $#4 Wem 29 $#4 %.27.8+& .494. $2 -$> +80/81 92.34$8-1>)


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5 DIPOLE CALCULATION

6> 8 18>$ >$4% (4 (80$ $2 *81*/18$4 $#4 3-%214 +2+40$ 92. 48*# >08%>#2$ >8X43 -0$40 .4>$8.$> 9-14 %.4X-2/>1J *2114*$43 803 $#40 +8G4 $#4 +480 X81/4 -0 2.34. $27-X4 $#-> (8J 80 4>$-+8$4 29 $#4 $4+%4.8$/.4 803 40$.2%-* 4994*$> 3/4 $2 $#440X-.20+40$ 92.+43 ,J $#4 >21X40$)

B.48$4 8 04( 92134. 803 *2%J $#4 .4>$8.$ 9-14> 803 $#4 2$#4. 044343 9-14> -0 $#->3-.4*$2.J&

mkdir DIPOLE_CALCULATIONcp ../ PRODUCTION-RUN/RESTART.* .cp ../ PRODUCTION-RUN/gromos* .cp ../ PRODUCTION-RUN/cpmd.inp dipole.inpcp ../PRODUCTION-RUN/LATEST .

803 +23-9J $#4 -0%/$ 9-14 $2 *81*/18$4 $#4 3-%214 +2+40$ 8> J2/ #8X4 148.0$ -0 $#4>4*203 %8.87.8%#&

n

oBC;Dp;;;V=`$ 1-04 29 $#4 9-14 S6,.%3 @!"#$%& (&" ) *"!+,- +#"./0,#&" 12.!01#""./#3#14567589:1;$*1*"!+


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!"#$%& (&" ) *"!+,- +#"./0,#&" 12.!01#""./#3#14567589:1;$*1*"!+G-%%43 $#-> %.2*43/.4 ,J />-07 $#4 G4J(2.3

DIPOLE DYNAMICS SAMPLE1000-0 $#4 %.4X-2/> BC *81*/18$-20) `/*# 8 G4J(2.3 +8G4> BC;D >8X4 $#4*22.3-08$4> 29 $#4 3-%214 +2+40$> 4X4.J "ZZZ >$4%> 20 8 9-14 *81143 DmCgS=) 604a8+%14 -> >8X43 -0 $#4 92134.&

/work/Tutorial/ACETONE/9-CPMD-MM/4-PRODUCTION-RUN/DIPOLE/

i2(4X4.H $#4>4 X81/4> 8.4 %218.-?8$-20> M-0 8)/)N& $#4J #8X4 $2 ,4 +/1$-%1J ,J $#4X21/+4 $2 2,$8-0 $#4 *2..4*$ X81/4> 29 $#4 3-%214 -0 8)/)

6$ $#-> %2-0$ J2/ #8X4 201J $2 4a$.8*$ 48*# X81/4 29 $#4 3-%214 +2+40$&

grep -B 1 -A 4 "X Y" dipole1.outgrep -B 1 -A 4 "X Y" dipole2.out

803 *81*/18$4 $#4 8.-$#+4$-* +480 D)

T#8$ -> $#4 3-994.40*4 (-$# .4>%4*$ $#4 X81/4 -0 X8*//+ (4 *81*/18$4 -0 $#4>4*203 %8.87.8%#q

T#8$ -> $#4 _/81-$8$-X4 .48>20 29 >/*# 8 3-994.40*4q

21X40$ 4994*$ *80 ,4 >4%8.8$43 -0 $(2 3-994.40$ *2+%2040$>& $#4742+4$.J X8.-8$-20 29 $#4 >21/$4 (-$# .4>%4*$ $2 $#4 78> %#8>4 M$4+%4.8$/.44994*$NH 803 $#4 3-994.40$ %218.-?8$-20 29 $#4 (8X49/0*$-20)i2( *2/13 J2/ %.2*443 -9 J2/ (80$43 $2 -340$-9J $#4 *20$.-,/$-20 29 $#4 $(2%8.$>q

QMMM Tutorial Ws10 11

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