exercises:2014_ethz_mmm:nacl_md
Observer NaCl dissociation
Perform a MD simulation of NaCl in water by running the input-file NaCl_in_water.inp
.
Use VMD to calculate the Na-Cl distance for each frame of the trajectory. This can be done in the following way:
- Load the trajectory with VMD
- Select
Extensions
→Analysis
→Radial Pair Distribution Function
from the menu - Within the $g(r)$-dialog select
Utilities
→Set unit cell dimensions
from the menu - Set the lengths a,b, and c to the value 12.413800, and click
Set unit cell
- Close the $g(r)$-dialog
- Fold back periodic images by typing:
pbc wrap -centersel “element Na” -center com -all
- Select
Mouse
→Label
→Bonds
from the menu - Click successively on the Na and the Cl atom
- Select
Graphics
→Labels…
from the menu - Select
Bonds
from the drop-down on the top left - Go to the tab
Graph
- Click
Save
to store the distance-trajectory
Plot the obtained distance-trajectory. Does the dissociation occur? If it occurs, does the actual transition happens quickly ? Is dissociation a likely or rare event ? Do you expect an activation energy ?
You should run this calculation on 4 cores with
bsub -n 4
.
Required Files
- NaCl_in_water.inp
&GLOBAL PROJECT NaCl-Free RUN_TYPE MD &END GLOBAL &MOTION &MD ENSEMBLE NVT TIMESTEP 0.5 STEPS 200000 TEMPERATURE 350 &THERMOSTAT &NOSE LENGTH 3 YOSHIDA 3 TIMECON 1000 MTS 2 &END NOSE &END &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 &EACH MD 20 &END &END &VELOCITIES OFF &END VELOCITIES &FORCES OFF &END FORCES &RESTART_HISTORY OFF &END RESTART_HISTORY &RESTART OFF &END RESTART &END PRINT &END MOTION &FORCE_EVAL METHOD FIST &MM &FORCEFIELD &SPLINE EMAX_SPLINE 300000.0 &END &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 Na CHARGE 1.0 &END CHARGE &CHARGE ATOM Cl CHARGE -1.0 &END CHARGE &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 &LENNARD-JONES atoms Na Na EPSILON [kcalmol] 0.0469 SIGMA [angstrom] 2.7275 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms Na O EPSILON [kcalmol] .08445 SIGMA [angstrom] 2.93 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms Na H EPSILON [kcalmol] .0464 SIGMA [angstrom] 1.5637 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms Na Cl EPSILON [kcalmol] .0838 SIGMA [angstrom] 3.63 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms Cl Cl EPSILON [kcalmol] 0.150 SIGMA [angstrom] 4.54 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms Cl O EPSILON [kcalmol] .151 SIGMA [angstrom] 3.84 RCUT [angstrom] 11.4 &END LENNARD-JONES &LENNARD-JONES atoms Cl H EPSILON [kcalmol] .083 SIGMA [angstrom] 2.47 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 12.4138 12.4138 12.4138 &END CELL &COORD O 1.1753544421905696E+01 4.4021851582586935E+00 7.9157840505153452E+00 H2O H 1.2340708249225194E+01 3.6883791978006242E+00 8.1993630993470603E+00 H2O H 1.1333172679938164E+01 3.8050318217272174E+00 7.2568637081413323E+00 H2O O 1.1014668880096623E+01 7.3042865500623817E+00 1.5990673397287788E+01 H2O H 1.0569187724590568E+01 6.6345975947947693E+00 1.5547591289605375E+01 H2O H 1.1898462021703027E+01 6.9874187796347469E+00 1.6036139720330969E+01 H2O O 1.2689782744905673E+00 6.6305310822204291E+00 3.8552255308181183E+00 H2O H 1.6331787505516266E+00 7.5407334033566018E+00 3.8990549604441207E+00 H2O H 2.0695006552397186E+00 6.0919818384977980E+00 3.4701014630706695E+00 H2O O 1.4178648518519008E+01 -5.4114420257859823E+00 9.0104448041665517E+00 H2O H 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2.4860458939795342E+00 H2O O 1.2422237951227883E+01 9.0346188032113839E-01 1.4858124935094497E+00 H2O H 1.2774907114847005E+01 7.9492905489321919E-01 2.3876055579074382E+00 H2O H 1.2383980110238154E+01 1.2639047505481145E-02 1.1711072142709946E+00 H2O O -1.9573950131095728E+00 2.6547233003600650E+00 6.3264685386946971E+00 H2O H -1.5890515349546790E+00 2.5049832646796166E+00 5.4377691277090836E+00 H2O H -2.6601680989277559E+00 2.0455377964092993E+00 6.3910371192140198E+00 H2O O -5.1746639502257485E+00 6.3268173165266930E+00 3.4022453265951325E+00 H2O H -5.8538826533083252E+00 6.0630475658559417E+00 4.0593847493701283E+00 H2O H -4.5456200014420274E+00 5.5948800178610094E+00 3.6466245011307188E+00 H2O O -1.7301550732454403E+00 9.4433133588285223E+00 8.2730143525629956E+00 H2O H -2.3588285739544199E+00 8.7002435560310936E+00 8.3843236064855855E+00 H2O H -2.1404889687710758E+00 1.0047127016482493E+01 8.9211555005887586E+00 H2O O 9.0552712375692934E+00 6.5294172265623143E+00 1.3742439694437869E+00 H2O H 8.3516076276067128E+00 6.3289151269823343E+00 2.0304907300642321E+00 H2O H 8.6528091280456980E+00 6.1831779653637149E+00 5.4298333174784219E-01 H2O O 4.5813760239127364E+00 4.1843345295343770E+00 1.6253526169022317E+00 H2O H 5.3727323765311770E+00 3.6298864387852703E+00 1.7138976863611635E+00 H2O H 4.6395747674616947E+00 4.3116322589753313E+00 6.3887219177749843E-01 H2O O 1.2947678437786887E+00 3.0271301953495872E-01 6.7378909919380270E+00 H2O H 3.1428367266724405E-01 4.5252218318749998E-01 6.7605145342793884E+00 H2O H 1.4651549989733721E+00 4.4724440682281402E-02 7.6184299786305614E+00 H2O O 2.2801010341157997E+00 4.5384374803766505E+00 -2.4223048356780224E+00 H2O H 2.0734054267726179E+00 3.6882567015458987E+00 -2.9666204618216470E+00 H2O H 2.5231047554518509E+00 5.2235789091310938E+00 -3.1134597962105883E+00 H2O O 3.7181632387798422E+00 1.3194671983555407E+01 2.1247302219660935E+00 H2O H 4.6221675287950585E+00 1.3097092431390625E+01 1.7939883243389010E+00 H2O H 3.2943497598348452E+00 1.3194908989088310E+01 1.2280237106837808E+00 H2O O 8.8760226994556335E-01 9.0819224935268252E+00 -4.9139340386609893E+00 H2O H 6.5645671723934040E-01 8.2903238990744885E+00 -5.4378003156474533E+00 H2O H 5.8843124393715890E-02 9.2202134104728284E+00 -4.4441892901661255E+00 H2O O 1.1597624822673641E+01 1.6904970546553898E+01 1.8174920862357313E+00 H2O H 1.2296467925610532E+01 1.7299711348881257E+01 1.2631420756029890E+00 H2O H 1.0851674042026399E+01 1.6978470962780285E+01 1.1636392443535732E+00 H2O O 1.3687809934453169E+01 1.2505476198613239E+01 3.9130051114462949E+00 H2O H 1.4539114519746876E+01 1.2552958854294646E+01 3.5281360273279936E+00 H2O H 1.3943283510045202E+01 1.2638239442171317E+01 4.8024112307295050E+00 H2O O -2.0127124384156674E+00 1.4456792042391635E+01 9.3689965302971068E+00 H2O H -1.2613367153937676E+00 1.3868330798915297E+01 9.5235783609143425E+00 H2O H -2.1313935694969701E+00 1.4494082421039327E+01 8.3588717975939772E+00 H2O O 5.9282480309534415E+00 2.1805080018332679E+00 4.7215454301010942E+00 H2O H 6.4216163069448253E+00 2.4503801200770838E+00 3.8999417372827963E+00 H2O H 5.5064601702213665E+00 1.3017508101133179E+00 4.5015046675505532E+00 H2O O 1.3855624950094682E-02 6.7674752704789931E+00 6.4172582115352652E+00 H2O H -3.9884540327593410E-01 5.9879627341341282E+00 6.8897045580221494E+00 H2O H 1.6576784524421465E-01 6.4353752097379919E+00 5.5228784846639938E+00 H2O O 1.4501812945221763E+01 3.3923060631855058E+00 3.0756235664424216E+00 H2O H 1.3706746681864210E+01 3.4193537022149547E+00 2.5497917586387699E+00 H2O H 1.5269466984949403E+01 3.1093971613675038E+00 2.5273427220944495E+00 H2O Na 1.0978482003279533E+01 9.1862595374996374E+00 1.3069121663365122E+01 NAP Cl 1.3489457703231567E+01 1.0346547591020910E+01 1.2149103773398551E+01 CLM &END COORD &COLVAR &DISTANCE ATOMS 190 191 &END DISTANCE &PRINT &END &END COLVAR &TOPOLOGY CONNECTIVITY GENERATE &GENERATE BONDLENGTH_MAX 7 &END &END &END SUBSYS &END FORCE_EVAL
exercises/2014_ethz_mmm/nacl_md.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1