# Open SourceMolecular Dynamics

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exercises:2018_ethz_mmm:h2o_md

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# Molecular dynamics of water

In this exercise we will focus on the calculation of the self-diffusion coefficient for water

max@qmobile:~$cd ; cd EXERCISES max@qmobile:~$ wget https://polybox.ethz.ch/index.php/s/ULaq6rjhg4Pu63A
max@qmobile:~$unzip exercise_2.1.zip max@qmobile:~$ cd exercise_2.1

This exercise is mostly taken by a previous lab session by Marcella Iannuzzi, UZH, who should be credited and acknowledged here.

The simulation is run in classical molecular dynamics, using the force field used in 10.1063/1.1884609 to ab initio calculations of the $\text{H}_2\text{O}$ molecule.

The input file looks like that:

md300.inp
#
# MD of liquid water,
# using FF parameters from Praprotnik et al.
#

@SET SYSTEM T300

&GLOBAL
PROJECT ${SYSTEM} RUN_TYPE MD IOLEVEL LOW &PRINT PHYSCON &END PRINT &END GLOBAL &FORCE_EVAL METHOD FIST &MM &FORCEFIELD &BEND ATOMS H O H KIND HARMONIC K [rad^-2kcalmol] 110.0 THETA0 [deg] 104.52 &END BEND &BOND ATOMS O H KIND HARMONIC K [angstrom^-2kcalmol] 900.0 R0 [angstrom] 0.9572 &END BOND &CHARGE ATOM O CHARGE -0.834 &END CHARGE &CHARGE ATOM H CHARGE 0.417 &END CHARGE &NONBONDED &LENNARD-JONES atoms O O EPSILON [kcalmol] 0.152073 SIGMA [angstrom] 3.1507 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms O H EPSILON [kcalmol] 0.0836 SIGMA [angstrom] 1.775 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms H H EPSILON [kcalmol] 0.04598 SIGMA [angstrom] 0.400 RCUT [angstrom] 11.4 &END LENNARD-JONES &END NONBONDED &END FORCEFIELD &POISSON &EWALD EWALD_TYPE spme ALPHA .3 GMAX 12 O_SPLINE 6 &END EWALD &END POISSON &END MM &SUBSYS &CELL ABC 9.865 9.865 9.865 &END CELL &COORD O 4.0990771611739696E+00 2.8633390287706875E+00 -1.6649750693973509E+01 H2O H 3.6198825143472750E+00 2.9036335565407616E+00 -1.5786648392717291E+01 H2O H 3.3938346757245652E+00 2.6337360930791434E+00 -1.7258942999974757E+01 H2O O 2.0552971764987920E+01 -6.0317716888860673E-01 1.5803161825113377E+00 H2O H 2.1120490846876077E+01 1.8081944903699243E-01 1.5972671732140640E+00 H2O H 2.0893915175102396E+01 -1.1019809737906978E+00 2.2954442847330800E+00 H2O O -7.9877938931079253E+00 -4.1105886694798226E+00 5.1753650941730527E+00 H2O H -8.8790878338731307E+00 -4.3113400305239749E+00 4.7757679757154712E+00 H2O H -8.2891098658871574E+00 -3.8515146034780807E+00 6.0560547138619309E+00 H2O O -1.5699295004190399E+00 -1.1419760510561048E+01 3.6129811814629091E+00 H2O H -1.2515766648456859E+00 -1.1923591199013609E+01 4.3578597300341348E+00 H2O H -1.6014794034952906E+00 -1.0516592744819420E+01 3.8884643815900621E+00 H2O O 1.4346361535163705E+01 5.7379597570369754E+00 2.6136480784137825E+00 H2O H 1.3652893679436762E+01 6.3630082232359664E+00 2.2771706319341090E+00 H2O H 1.4142392462670498E+01 4.8901695938881256E+00 2.2500603744101371E+00 H2O O -1.2978502407406938E+00 -4.4197376154960653E+00 -1.0108922244726434E+01 H2O H -1.8209963244428125E+00 -4.0747449322863023E+00 -9.3928887615783125E+00 H2O H -1.8451970174557182E+00 -4.0605585415637524E+00 -1.0828278436385499E+01 H2O O 2.3505758212524612E+00 6.5988051487995394E+00 -9.0122820030981963E+00 H2O H 1.4916378847116123E+00 6.4099106638859480E+00 -8.5658667433350448E+00 H2O H 2.3259896427433664E+00 7.5392171863950361E+00 -9.0180780131236329E+00 H2O O -1.4312545906816201E+00 1.0119870177802614E+01 4.2355709830113553E-01 H2O H -1.9812309973608044E+00 9.3726251166317347E+00 7.5378044133890876E-01 H2O H -5.2677028459445807E-01 9.7434365832171981E+00 6.8082337693327510E-01 H2O O -7.2000125111789446E+00 -1.7297909920535137E+00 3.5519625527895298E+00 H2O H -7.5167017909363727E+00 -2.5625554479762518E+00 3.9663954244597615E+00 H2O H -7.4506425314478069E+00 -1.0888225237769447E+00 4.2397624267581158E+00 H2O O 1.0026382924586821E+01 6.4767710974957611E+00 2.3941661233133869E+00 H2O H 9.5657822147267115E+00 5.6711814281190902E+00 2.7635232090888051E+00 H2O H 9.6384789304574774E+00 7.1925052122997686E+00 2.8006359052237411E+00 H2O O 1.1844324850463268E+01 -2.0927058882474009E-01 -1.4065649668312794E+01 H2O H 1.2314749496538584E+01 4.4265839944891588E-01 -1.3587211076047117E+01 H2O H 1.1036049490850663E+01 -1.3482532936801822E-01 -1.3581077198077274E+01 H2O O -1.3112158228748623E+01 -6.2864535685630267E+00 2.0201791079602431E+00 H2O H -1.3342241444014668E+01 -6.7879338549113566E+00 1.2161643714725265E+00 H2O H -1.3917490102408042E+01 -6.4745955342905610E+00 2.5361963291835736E+00 H2O O 6.5504055434638353E+00 2.1722091632679059E+00 -5.2540920378685352E-01 H2O H 7.1181690032685019E+00 2.5160448913501052E+00 -1.2237604523620926E+00 H2O H 7.2032005514839970E+00 1.6132595514874122E+00 -8.4915330775898967E-02 H2O O 2.8728641994261084E+00 1.2463894784822655E+01 1.5766802157132808E+01 H2O H 3.5319661130868818E+00 1.2345097305742453E+01 1.6480886597851171E+01 H2O H 2.7260654590898588E+00 1.3425501065702791E+01 1.5689058285651134E+01 H2O O -4.7232088660258364E+00 6.1874970257059410E+00 -4.2010201320925882E+00 H2O H -5.7015580792394100E+00 6.3229099912716578E+00 -4.3313313722768019E+00 H2O H -4.5258103994562235E+00 6.2059968095552209E+00 -5.1454834292675624E+00 H2O O -1.1207108202024731E+01 1.2262911915342658E+01 -2.3602598361478542E+00 H2O H -1.1272681819601486E+01 1.2282332810869732E+01 -3.3705272042851795E+00 H2O H -1.0522707298067429E+01 1.1539271180629608E+01 -2.3426251777429385E+00 H2O O 1.0157679618370272E+01 -1.6491057241445276E+01 -3.8891647715560207E-01 H2O H 9.7050356527735868E+00 -1.6842658877059659E+01 -1.1648717278703189E+00 H2O H 9.5777475747466223E+00 -1.5735770228942069E+01 -1.4504538901147770E-01 H2O O -3.3867315013774526E+00 7.8050895970982230E+00 -8.3184507808782868E+00 H2O H -2.5883287464162126E+00 7.8752895157315681E+00 -7.7780603012568621E+00 H2O H -3.9367339883859653E+00 7.2104800149382875E+00 -7.8563335584074725E+00 H2O O 4.1388042326267591E+00 -1.5072806578102765E-01 1.4303824695133505E+00 H2O H 5.0472500573404178E+00 -4.8722470110749433E-01 1.4589770925283638E+00 H2O H 3.7467405608582829E+00 -6.3998028017083075E-01 2.1394965295434982E+00 H2O O 4.2595384151575244E+00 8.0363289325704235E-01 7.8672617022531943E+00 H2O H 4.8130766850341962E+00 1.2024067826714520E+00 7.1413687326139179E+00 H2O H 4.7953746600283598E+00 9.3924952891872560E-01 8.6335903258658764E+00 H2O O -4.5191738819706266E+00 4.8674040686154907E+00 -7.7424914554764745E-01 H2O H -3.9584835582169862E+00 4.1916762292422938E+00 -3.5632919560932813E-01 H2O H -5.3361240627326687E+00 4.6593170146920473E+00 -2.7748760122726546E-01 H2O O -4.6486190763083393E+00 1.0559684456132420E+01 2.4666697824632244E+01 H2O H -5.1718646071776799E+00 9.9061307184318412E+00 2.5191864943109294E+01 H2O H -5.2151318309590131E+00 1.0863848671746059E+01 2.4008154438222835E+01 H2O O -1.8920336095563112E-01 -1.9723082418168051E+01 -1.2331751859031851E+01 H2O H -6.9853839676937413E-01 -2.0510391457743804E+01 -1.2648106790669067E+01 H2O H -6.7178927685170767E-02 -1.9904341227137060E+01 -1.1401598461365145E+01 H2O O 8.6092522191222010E+00 -1.5300879172778661E+01 -6.2889540677378104E+00 H2O H 8.6164121625349033E+00 -1.5988040732713319E+01 -5.6163515969455950E+00 H2O H 7.8631907409852495E+00 -1.5565758302286353E+01 -6.8912232725417359E+00 H2O O 1.4533087231921096E+00 -1.3305185412448356E+01 -1.1916886354803323E+01 H2O H 1.5704975438853019E+00 -1.2389522343553942E+01 -1.1638778267823120E+01 H2O H 2.1592317355561943E+00 -1.3688032462538523E+01 -1.1445000291043685E+01 H2O O 2.9687705641225186E+00 -5.7847368452718690E+00 1.0198124958568776E+01 H2O H 2.1055313600020069E+00 -6.1369494659703072E+00 9.8643510074097875E+00 H2O H 2.7673476315489345E+00 -4.8175890711447638E+00 1.0261860604897310E+01 H2O O 2.1307179526981219E+00 9.0141614782957706E+00 8.8029803669936140E+00 H2O H 2.6906994240494826E+00 9.4300032870082422E+00 9.5306845691514326E+00 H2O H 2.5357829972259256E+00 9.3708237774629808E+00 7.9904382164776395E+00 H2O O -2.7590496648261693E+00 -3.1955215144759475E+00 -2.3261918496018064E+00 H2O H -3.3546076991918565E+00 -3.3511138435382928E+00 -3.1173095619864135E+00 H2O H -3.4116085527171047E+00 -3.3919867560013448E+00 -1.5671279742947930E+00 H2O O -7.9159449798759551E+00 1.8733590643400650E+00 -8.2162396984353716E+00 H2O H -8.7859157283547180E+00 2.2519209017166939E+00 -8.5544872930068880E+00 H2O H -7.2213059662322143E+00 2.0590146256161748E+00 -8.9557258250561773E+00 H2O O 7.4839506528220578E+00 1.2172260395768921E+01 5.0433745483595249E+00 H2O H 6.8305009483129693E+00 1.1483218223760431E+01 4.6766276844537620E+00 H2O H 6.9209089699397879E+00 1.2599276062084877E+01 5.7102955698020521E+00 H2O O -2.0365405094837961E+01 -1.2256879300334079E+01 6.2150050341365217E+00 H2O H -1.9797664340014357E+01 -1.2734530157707740E+01 6.7789740677763728E+00 H2O H -2.1192917559895324E+01 -1.2576379478142982E+01 6.7398537673836154E+00 H2O O 5.3894209467850960E+00 3.4139122557112409E+00 -3.3441897135960801E+00 H2O H 5.4941839731265079E+00 4.0025859745240160E+00 -2.5460134060473312E+00 H2O H 5.3456451321990039E+00 4.1287379135378721E+00 -3.9781343543418788E+00 H2O &END COORD &END SUBSYS &END FORCE_EVAL &MOTION &MD ENSEMBLE NVE TIMESTEP 0.5 STEPS 50000 TEMPERATURE 300 &PRINT &ENERGY &EACH MD 20 &END &END ENERGY &PROGRAM_RUN_INFO &EACH MD 20 &END &END PROGRAM_RUN_INFO &END PRINT &END MD &PRINT &TRAJECTORY SILENT FILENAME =${SYSTEM}.xyz
&EACH
MD 20
&END EACH
&END TRAJECTORY
&VELOCITIES ON
&EACH
MD 20
&END EACH
&END VELOCITIES
&FORCES OFF
&END FORCES
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&RESTART OFF
&END RESTART
&END PRINT
&END MOTION
1. Read the paper through section III to see which parameters are used for which interaction.
2. Recognize the parameters in the input file
3. Run the md300.in: the command is
cp2k.ssmp -i md300.in > md300.out
4. Postprocess the trajectory to compute mean square displacement and velocity-velocity correlation function
5. Extract the diffusion coefficients and compare the two approaches:
vel_autocorr.py T300-vel-1.xyz 3 10 100
vel_autocorr_plot.py vel_autocorr.out
mean_square_displ.py T300.xyz 3 10 100
msd_fit_and_plot.py mean_square_disp.out