exercises:2018_ethz_mmm:h2o_md
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exercises:2018_ethz_mmm:h2o_md [2018/03/02 05:25] – created dpasserone | exercises:2018_ethz_mmm:h2o_md [2018/03/02 14:58] – dpasserone | ||
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<note tip> | <note tip> | ||
- | All files of this exercise be downloaded directly from the wiki: {{exercise_2.1.zip|}} | + | All files of this exercise be downloaded directly from [[https://polybox.ethz.ch/ |
</ | </ | ||
Download the 2.1 exercise into your **EXERCISES** folder and unzip it. | Download the 2.1 exercise into your **EXERCISES** folder and unzip it. | ||
- | < | ||
- | max@qmobile: | ||
- | max@qmobile: | ||
- | max@qmobile: | ||
- | max@qmobile: | ||
- | </ | ||
+ | This exercise is mostly taken by a [[https:// | ||
+ | |||
+ | |||
+ | The simulation is run in classical molecular dynamics, using the force field used in [[doi> | ||
+ | |||
+ | The input file looks like that: | ||
+ | <code - md300.inp> | ||
+ | # | ||
+ | # MD of liquid water, | ||
+ | # using FF parameters from Praprotnik et al. | ||
+ | # | ||
+ | |||
+ | @SET SYSTEM T300 | ||
+ | |||
+ | &GLOBAL | ||
+ | PROJECT ${SYSTEM} | ||
+ | RUN_TYPE MD | ||
+ | IOLEVEL LOW | ||
+ | |||
+ | | ||
+ | &END PRINT | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | METHOD FIST | ||
+ | &MM | ||
+ | & | ||
+ | &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 | ||
+ | & | ||
+ | & | ||
+ | atoms O O | ||
+ | EPSILON [kcalmol] | ||
+ | SIGMA | ||
+ | RCUT [angstrom] 11.4 | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | atoms O H | ||
+ | EPSILON [kcalmol] 0.0836 | ||
+ | SIGMA [angstrom] 1.775 | ||
+ | RCUT [angstrom] 11.4 | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | atoms H H | ||
+ | EPSILON [kcalmol] | ||
+ | SIGMA | ||
+ | RCUT [angstrom] 11.4 | ||
+ | &END LENNARD-JONES | ||
+ | &END NONBONDED | ||
+ | &END FORCEFIELD | ||
+ | & | ||
+ | &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 | ||
+ | H 3.6198825143472750E+00 | ||
+ | H 3.3938346757245652E+00 | ||
+ | O 2.0552971764987920E+01 | ||
+ | H 2.1120490846876077E+01 | ||
+ | H 2.0893915175102396E+01 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 1.4346361535163705E+01 | ||
+ | H 1.3652893679436762E+01 | ||
+ | H 1.4142392462670498E+01 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 2.3505758212524612E+00 | ||
+ | H 1.4916378847116123E+00 | ||
+ | H 2.3259896427433664E+00 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 1.0026382924586821E+01 | ||
+ | H 9.5657822147267115E+00 | ||
+ | H 9.6384789304574774E+00 | ||
+ | O 1.1844324850463268E+01 | ||
+ | H 1.2314749496538584E+01 | ||
+ | H 1.1036049490850663E+01 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 6.5504055434638353E+00 | ||
+ | H 7.1181690032685019E+00 | ||
+ | H 7.2032005514839970E+00 | ||
+ | O 2.8728641994261084E+00 | ||
+ | H 3.5319661130868818E+00 | ||
+ | H 2.7260654590898588E+00 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 1.0157679618370272E+01 | ||
+ | H 9.7050356527735868E+00 | ||
+ | H 9.5777475747466223E+00 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 4.1388042326267591E+00 | ||
+ | H 5.0472500573404178E+00 | ||
+ | H 3.7467405608582829E+00 | ||
+ | O 4.2595384151575244E+00 | ||
+ | H 4.8130766850341962E+00 | ||
+ | H 4.7953746600283598E+00 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 8.6092522191222010E+00 | ||
+ | H 8.6164121625349033E+00 | ||
+ | H 7.8631907409852495E+00 | ||
+ | O 1.4533087231921096E+00 | ||
+ | H 1.5704975438853019E+00 | ||
+ | H 2.1592317355561943E+00 | ||
+ | O 2.9687705641225186E+00 | ||
+ | H 2.1055313600020069E+00 | ||
+ | H 2.7673476315489345E+00 | ||
+ | O 2.1307179526981219E+00 | ||
+ | H 2.6906994240494826E+00 | ||
+ | H 2.5357829972259256E+00 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 7.4839506528220578E+00 | ||
+ | H 6.8305009483129693E+00 | ||
+ | H 6.9209089699397879E+00 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 5.3894209467850960E+00 | ||
+ | H 5.4941839731265079E+00 | ||
+ | H 5.3456451321990039E+00 | ||
+ | &END COORD | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | |||
+ | &MOTION | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | &EACH | ||
+ | MD 20 | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | &EACH | ||
+ | MD 20 | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | FILENAME =${SYSTEM}.xyz | ||
+ | &EACH | ||
+ | MD 20 | ||
+ | &END EACH | ||
+ | &END TRAJECTORY | ||
+ | & | ||
+ | &EACH | ||
+ | MD 20 | ||
+ | &END EACH | ||
+ | &END VELOCITIES | ||
+ | &FORCES OFF | ||
+ | &END FORCES | ||
+ | & | ||
+ | &END RESTART_HISTORY | ||
+ | & | ||
+ | &END RESTART | ||
+ | & | ||
+ | &END MOTION | ||
+ | </ | ||
+ | |||
+ | <note tip> | ||
+ | - Read the paper through section III to see which parameters are used for which interaction. | ||
+ | - Recognize the parameters in the input file | ||
+ | - Run the **md300.in**: | ||
+ | - Postprocess the trajectory to compute mean square displacement and velocity-velocity correlation function | ||
+ | - Extract the diffusion coefficients and compare the two approaches (the instruction about the parameters: **./ | ||
+ | < | ||
+ | ./ | ||
+ | ./ | ||
+ | ./ | ||
+ | </ | ||
+ | <note important> | ||
+ | - look at the file T300-1.ener at the end of the simulation. It contains several quantities. Check the header! | ||
+ | - Using gnuplot, check the stability of the MD, you can also use < | ||
+ | - How do you interpret the oscillation of the potential energy? And of temperature? | ||
+ | - Compare the values of the diffusion coefficient with the two methods. Are they compatible? | ||
+ | - Look at the trajectories with vmd. Why are the particles " | ||
+ | - Copy md300.in into md200.in and change the system name and the initial temperature. Run the md. What is the final temperature? | ||
+ | - Copy md300.in into md400.in and change to 400 in the two places. Run the md. What is the final temperature? | ||
+ | - Check the temperature dependence of the diffusion coefficient. Plot the result. | ||
+ | </ | ||
exercises/2018_ethz_mmm/h2o_md.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1