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: Properties of Ice from Monte Carlo Simulations).
NaCl_in_water.inp. bsub -n 4.
This can be done in the following way:
Extensions → Analysis → Radial Pair Distribution Function from the menuUtilities → Set unit cell dimensions from the menuSet unit cellpbc wrap -centersel “element Na” -center com -allMouse → Label → Bonds from the menuGraphics → Labels… from the menuBonds from the drop-down on the top leftGraphSave to store the distance-trajectoryPlot 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 ?
The file is divided in 2 parts:
&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 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 1.4017865457100729E+01 -4.5904322660861938E+00 8.5501233014882416E+00 H2O
H 1.3483940372104527E+01 -5.5149586247719489E+00 9.6651833370983109E+00 H2O
O 1.1452264597040871E+01 1.0887873649551166E+01 3.2084689203614567E+00 H2O
H 1.1967066565244300E+01 1.1445433261897549E+01 3.7649461013539907E+00 H2O
H 1.0557245919373200E+01 1.1324397817482820E+01 3.2777714519474994E+00 H2O
O 5.4034513877480865E+00 -5.6934982866713590E-01 4.1911517278163561E+00 H2O
H 4.5483481626988249E+00 -1.0111873129240894E+00 3.9370590485310837E+00 H2O
H 5.8745595810397493E+00 -1.3341026429777330E+00 4.5979862398760112E+00 H2O
O 1.0057227115948024E+01 1.6229149149924339E+01 2.3925996591412417E+01 H2O
H 9.2698383115214416E+00 1.6823858684663453E+01 2.4105928499738823E+01 H2O
H 9.7419675944524666E+00 1.5633504273481041E+01 2.3231028348851662E+01 H2O
O 8.8677965379732058E+00 1.1265135417657429E+01 9.3927083078931553E+00 H2O
H 8.0047959048088178E+00 1.0873622086214446E+01 9.1123875773689491E+00 H2O
H 8.9279753280405316E+00 1.1225261501792545E+01 1.0383859150647918E+01 H2O
O 3.4080063685919972E+00 3.8281480273536057E+00 5.2014798452536946E+00 H2O
H 4.2321572059400339E+00 3.3876157648413292E+00 5.0447755744929355E+00 H2O
H 2.8950992358414052E+00 3.6968963428074426E+00 4.3257317504719071E+00 H2O
O 3.2104267444392396E+00 1.0140965941598806E+01 5.4422954259256739E+00 H2O
H 2.7530338415002489E+00 9.8998848654428535E+00 4.5986562717830264E+00 H2O
H 2.4556531455595496E+00 1.0441077526316068E+01 6.0489660829709155E+00 H2O
O 4.0963537625725674E+00 8.0917539958074993E+00 1.0134372895799503E+01 H2O
H 3.3568409082389805E+00 7.7228723438249398E+00 9.6190434068097073E+00 H2O
H 4.3609077527930795E+00 8.7918074613791131E+00 9.5341819775764804E+00 H2O
O -5.5665924947641816E+00 7.3067204927259235E+00 -1.9883598323724647E+00 H2O
H -6.5034019372924075E+00 7.6053625026413805E+00 -2.0987994044233194E+00 H2O
H -5.3150004199521055E+00 7.2870401654684125E+00 -2.9091914567841886E+00 H2O
O 1.1676278913686788E+01 1.5298249986393781E+01 1.6383563437817887E+01 H2O
H 1.2587464831334719E+01 1.5435371673523250E+01 1.6628396684857599E+01 H2O
H 1.1591655936254574E+01 1.5853475115631859E+01 1.5539570840387995E+01 H2O
O 1.4061976353495059E+01 9.2245551836285333E+00 3.3628338059328726E+00 H2O
H 1.3450288603772332E+01 9.9005997350888588E+00 3.6811276936530497E+00 H2O
H 1.4189484851779527E+01 9.4617482111957045E+00 2.4386940515991853E+00 H2O
O 4.0459889100093029E+00 6.5177362398102456E+00 2.5732744024062764E+00 H2O
H 3.5401823659550020E+00 6.8224242718743318E+00 1.8061354812594488E+00 H2O
H 4.3061858864345899E+00 5.6596188680600106E+00 2.2544873571934723E+00 H2O
O 5.3942555383779709E+00 5.9921077919598975E+00 5.5479964555191721E+00 H2O
H 4.5696452524535074E+00 5.5450869700159764E+00 5.3861090187122072E+00 H2O
H 5.8041847517531799E+00 5.4340702269751437E+00 6.2406501382283697E+00 H2O
O 1.1083204000766642E+01 -5.5817706946529055E-01 1.9012213049501533E+01 H2O
H 1.0766380933295238E+01 -1.5297161070578786E+00 1.9234395970879390E+01 H2O
H 1.0301075722148791E+01 -2.2202937914601956E-01 1.8534569531285435E+01 H2O
O 8.0791998553974889E+00 7.3510519348550423E+00 -4.3460713060718152E+00 H2O
H 7.6759201146623637E+00 6.6038372265123675E+00 -4.9207705506418193E+00 H2O
H 7.7374893085203249E+00 8.0604176451161393E+00 -4.9062736907587210E+00 H2O
O 9.0599466123812089E+00 -1.1429275580287841E+00 1.2359299045122484E+01 H2O
H 8.1731340512894715E+00 -8.4813525786179789E-01 1.2153183944704283E+01 H2O
H 9.3354403117752280E+00 -3.0344035057609919E-01 1.2782538396372816E+01 H2O
O 7.3128194079715705E+00 1.0087518663499242E+01 4.6982644114541596E+00 H2O
H 8.0618288813246686E+00 9.7202011976988612E+00 5.2055576656885707E+00 H2O
H 7.2561941364348446E+00 9.4520654638910369E+00 3.9300655501395521E+00 H2O
O 7.9081332415871142E+00 1.3493631056974145E+01 -1.7023111105913979E+00 H2O
H 7.9296786531697769E+00 1.2737626146720082E+01 -2.3310520486375612E+00 H2O
H 8.8258690050704462E+00 1.3833681600410728E+01 -1.8106172707798294E+00 H2O
O 3.0343124639160681E+00 -5.1228535011701286E+00 2.0672656222212285E-01 H2O
H 3.6229508004737765E+00 -5.0138795773847775E+00 -5.4302739923341814E-01 H2O
H 2.4430790352456935E+00 -4.4202075922270847E+00 3.0522044152506863E-02 H2O
O 6.1403349808958954E+00 1.3553394843140385E+00 3.5842881823535444E-01 H2O
H 6.8199298055993873E+00 1.2490493021132034E+00 -3.7837775822664221E-01 H2O
H 5.4136904105251489E+00 7.7533952254521210E-01 -2.0200981294157712E-02 H2O
O 1.1818413215892830E+01 6.0342992643590794E+00 1.0161892222232515E+01 H2O
H 1.1984376256547076E+01 5.5829933767316451E+00 9.3073360179197255E+00 H2O
H 1.1359766709069046E+01 5.3662463571587269E+00 1.0616419288216939E+01 H2O
O 2.0056876408425651E+01 1.4884394953405629E+01 1.4785031476074208E+01 H2O
H 2.0914912760107462E+01 1.4685896617430362E+01 1.4355413941592094E+01 H2O
H 1.9453366228760853E+01 1.4584456213825597E+01 1.4072600004011722E+01 H2O
O 1.4255904314186182E+01 2.1756635286452664E+00 -2.0579711479072640E-01 H2O
H 1.3805349503679688E+01 2.9528386128226822E+00 -4.8295360444351881E-01 H2O
H 1.3569123093943860E+01 1.6551351670404930E+00 2.5853592700899408E-01 H2O
O 7.6086778925713991E+00 5.1699928912468014E+00 -4.9638488295799893E-01 H2O
H 6.7781094300338305E+00 4.7946702112099135E+00 -5.7099171112346547E-01 H2O
H 7.3607191780882069E+00 5.9446369058096078E+00 -1.1349785326398023E+00 H2O
O 1.2020909502195277E+01 -1.7339290247423964E-02 9.4954974980296427E+00 H2O
H 1.1610474491815115E+01 -5.8818398715592990E-01 8.8344295516358979E+00 H2O
H 1.2553354307793303E+01 -6.6079275446538310E-01 9.9480054031386871E+00 H2O
O 1.6125272725360077E+01 1.4144118398901252E+01 1.0018485667325464E+01 H2O
H 1.5358446740855484E+01 1.4240179363530874E+01 1.0535697576993389E+01 H2O
H 1.6448807629032782E+01 1.3331588379115230E+01 1.0446181193701090E+01 H2O
O 2.3784433487149315E+00 1.1076368066157427E+01 8.7625696673092115E+00 H2O
H 2.1625304504587910E+00 1.0952073635783481E+01 9.7050954143082162E+00 H2O
H 2.0943392125095457E+00 1.0240369700452140E+01 8.3110192332165411E+00 H2O
O -2.6202486540065455E+00 1.4011749466336040E+01 1.3270861019058238E+01 H2O
H -1.7969706446069031E+00 1.3789345701846116E+01 1.3728013603660095E+01 H2O
H -2.2451970406009290E+00 1.4582611904820402E+01 1.2604464854929647E+01 H2O
O 6.2324420266564085E+00 3.2029433865186432E+00 9.3624276034988796E+00 H2O
H 5.5245049044418595E+00 2.5909899487287613E+00 9.1683914888494868E+00 H2O
H 6.9326197318002958E+00 2.5510489529092562E+00 9.5829330178095926E+00 H2O
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H 3.8419378351717626E+00 -4.0825662269384883E-01 -4.2322475898066978E+00 H2O
H 4.3556294121150945E+00 -6.8993416251599368E-02 -5.6172218051143767E+00 H2O
O 7.9052074989079832E+00 9.2948507676364112E-01 6.8291165660776105E+00 H2O
H 7.8329518120522037E+00 -7.3239505544300101E-02 6.8912772475034485E+00 H2O
H 7.1525080724220409E+00 1.0968384122968011E+00 6.2602612138667606E+00 H2O
O -1.0398132450870442E+01 2.7421665494827967E+00 7.9771104768784520E+00 H2O
H -1.0118440415027528E+01 1.8744659613464276E+00 7.6017037030346311E+00 H2O
H -1.0281068420389072E+01 3.3134252506494537E+00 7.2268217324361457E+00 H2O
O 1.7533809170986110E+01 8.3996884769277145E+00 7.0775230417456161E+00 H2O
H 1.6717092384419313E+01 8.7623151811233821E+00 6.7539563539362222E+00 H2O
H 1.7543220685207306E+01 7.5975629140922765E+00 6.6031835390524032E+00 H2O
O 9.5953872749122588E+00 8.8268858183947163E+00 5.4382850332669426E+00 H2O
H 1.0238607616030258E+01 8.4651601433012935E+00 6.0669495439702921E+00 H2O
H 9.9642126418558927E+00 8.3861554514842460E+00 4.5985338458206115E+00 H2O
O 8.7359549409803368E+00 1.1920084550572563E+01 1.5852925009243505E+01 H2O
H 8.0301244117232340E+00 1.1463505274064429E+01 1.6306205471860146E+01 H2O
H 8.4028868462495421E+00 1.2798595199963700E+01 1.5745710868385185E+01 H2O
O 1.1342387483264285E+00 5.2005653993259084E+00 1.2366711127094838E+01 H2O
H 1.1431529635020097E+00 5.1320701266105537E+00 1.1414135555772207E+01 H2O
H 1.8795654384061717E+00 5.8743639708810225E+00 1.2435944020993762E+01 H2O
O 4.3425048054329363E+00 -3.8372902380130947E-01 -6.8811389491354846E-01 H2O
H 4.9653001666371264E+00 -1.1389448951649650E+00 -7.2877424200227259E-01 H2O
H 3.4795887915173225E+00 -7.7707860793195005E-01 -7.2294198067867210E-01 H2O
O 6.1470830049255065E+00 1.0085545639361571E+01 1.2268736915938019E+01 H2O
H 6.5254072780528931E+00 9.2877004313627101E+00 1.2081645015830070E+01 H2O
H 6.1233735619293537E+00 1.0012722305828664E+01 1.3215459072130194E+01 H2O
O 6.6165176287786709E+00 1.0529619266394285E+01 8.1992767508908582E+00 H2O
H 5.9988949867397610E+00 9.7988783921300175E+00 7.8716578752856874E+00 H2O
H 6.1011758707194499E+00 1.1339592595597649E+01 8.1245330556548261E+00 H2O
O 8.7448930318205207E+00 4.2035778229574090E+00 1.6667592832738887E+01 H2O
H 9.6172437182814239E+00 4.0012818436346835E+00 1.7026462880666656E+01 H2O
H 8.5879634837153418E+00 3.5408621470564983E+00 1.5950016180164910E+01 H2O
O 9.5857210543430735E+00 -4.3492649059459136E+00 1.0605138978330569E+01 H2O
H 8.7011778178526846E+00 -4.3054052892968100E+00 1.0155639446375634E+01 H2O
H 9.8328305198610977E+00 -5.2662332273982075E+00 1.0325404642237823E+01 H2O
O 7.1655754815424828E+00 4.8164058031273917E+00 6.9827991623818564E+00 H2O
H 6.9362457515784772E+00 4.1932819035984634E+00 7.6424112374177593E+00 H2O
H 7.6766494125251219E+00 4.2500051222557786E+00 6.3821210756773006E+00 H2O
O 4.8297972570762884E+00 4.2070042207196598E+00 1.1472942891352414E+01 H2O
H 5.2224983419581656E+00 3.8616217919542937E+00 1.0624799108046785E+01 H2O
H 3.8202638973321665E+00 4.1557641669173115E+00 1.1130561361855788E+01 H2O
O 6.1141281181639009E+00 -3.9160509004418516E+00 2.2361959985724997E+00 H2O
H 6.6741010314616558E+00 -4.6633655391585531E+00 2.4374748071535737E+00 H2O
H 5.1417813696946197E+00 -4.2737431164787880E+00 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
&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