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exercises:2016_ethz_mmm:nacl_md

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: 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:

  1. Load the trajectory with VMD
  2. Select ExtensionsAnalysisRadial Pair Distribution Function from the menu
  3. Within the $g(r)$-dialog select UtilitiesSet unit cell dimensions from the menu
  4. Set the lengths a,b, and c to the value 12.413800, and click Set unit cell
  5. Close the $g(r)$-dialog
  6. Fold back periodic images by typing: pbc wrap -centersel “element Na” -center com -all
  7. Select MouseLabelBonds from the menu
  8. Click successively on the Na and the Cl atom
  9. Select GraphicsLabels… from the menu
  10. Select Bonds from the drop-down on the top left
  11. Go to the tab Graph
  12. 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
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
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
O    4.7056900888016964E+00   -2.1740031489115283E-01   -4.7455853617226955E+00 H2O
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
exercises/2016_ethz_mmm/nacl_md.txt · Last modified: 2016/02/03 10:54 (external edit)