====== Observe NaCl dissociation ====== This short task will help you to familiarize with Molecular Dynamics simulations. The simulation is based on forcefields, with parameters of the same type of those we used for ice (See: [[exercises:2015_ethz_mmm:monte_carlo_ice|Properties of Ice from Monte Carlo Simulations]]). * You can perform the simulation of NaCl in water by running the input-file: ''NaCl_in_water.inp''. You should run this calculation on 4 cores with ''bsub -n 4''. * Then 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 ? ====== Required Files ====== The file is divided in 2 parts: * GLOBAL & MOTION : Specify the parameters of the simulations * FORCE EVAL : Specifies the system geometry and interactions between atoms &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 Na 1.0978482003279533E+01 9.1862595374996374E+00 1.3069121663365122E+01 NAP Cl 1.3489457703231567E+01 1.0346547591020910E+01 1.2149103773398551E+01 CLM 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 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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 &END COORD &COLVAR &DISTANCE ATOMS 1 2 &END DISTANCE &PRINT &END &END COLVAR &TOPOLOGY CONNECTIVITY GENERATE &GENERATE BONDLENGTH_MAX 7 &END &END &END SUBSYS &END FORCE_EVAL