exercises:2016_ethz_mmm:nacl_md
Differences
This shows you the differences between two versions of the page.
— | exercises:2016_ethz_mmm:nacl_md [2020/08/21 10:15] (current) – created - external edit 127.0.0.1 | ||
---|---|---|---|
Line 1: | Line 1: | ||
+ | ====== Observe NaCl dissociation ====== | ||
+ | This short task will help you to familiarize with Molecular Dynamics simulations. The simulation is based on forcefields, | ||
+ | |||
+ | * You can perform the simulation of NaCl in water by running the input-file: '' | ||
+ | |||
+ | <note tip> | ||
+ | You should run this calculation on 4 cores with '' | ||
+ | </ | ||
+ | |||
+ | * 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 '' | ||
+ | - Within the $g(r)$-dialog select '' | ||
+ | - Set the lengths a,b, and c to the value 12.413800, and click '' | ||
+ | - Close the $g(r)$-dialog | ||
+ | - Fold back periodic images by typing: '' | ||
+ | - Select '' | ||
+ | - Click successively on the Na and the Cl atom | ||
+ | - Select '' | ||
+ | - Select '' | ||
+ | - Go to the tab '' | ||
+ | - Click '' | ||
+ | |||
+ | 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 | ||
+ | <code - NaCl_in_water.inp> | ||
+ | &GLOBAL | ||
+ | PROJECT NaCl-Free | ||
+ | RUN_TYPE MD | ||
+ | &END GLOBAL | ||
+ | |||
+ | &MOTION | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | | ||
+ | | ||
+ | MTS 2 | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | &EACH | ||
+ | MD 20 | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | &EACH | ||
+ | MD 20 | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | MD 20 | ||
+ | & | ||
+ | &END | ||
+ | & | ||
+ | &END VELOCITIES | ||
+ | &FORCES OFF | ||
+ | &END FORCES | ||
+ | & | ||
+ | &END RESTART_HISTORY | ||
+ | & | ||
+ | &END RESTART | ||
+ | &END PRINT | ||
+ | &END MOTION | ||
+ | |||
+ | & | ||
+ | METHOD FIST | ||
+ | &MM | ||
+ | & | ||
+ | &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 | ||
+ | & | ||
+ | & | ||
+ | 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 | ||
+ | & | ||
+ | atoms Na Na | ||
+ | EPSILON [kcalmol] | ||
+ | SIGMA | ||
+ | RCUT [angstrom] 11.4 | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | atoms Na O | ||
+ | EPSILON [kcalmol] | ||
+ | SIGMA | ||
+ | RCUT [angstrom] 11.4 | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | atoms Na H | ||
+ | EPSILON [kcalmol] | ||
+ | SIGMA | ||
+ | RCUT [angstrom] 11.4 | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | atoms Na Cl | ||
+ | EPSILON [kcalmol] | ||
+ | SIGMA | ||
+ | RCUT [angstrom] 11.4 | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | atoms Cl Cl | ||
+ | EPSILON [kcalmol] | ||
+ | SIGMA | ||
+ | RCUT [angstrom] 11.4 | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | atoms Cl O | ||
+ | EPSILON [kcalmol] | ||
+ | SIGMA | ||
+ | RCUT [angstrom] 11.4 | ||
+ | &END LENNARD-JONES | ||
+ | & | ||
+ | atoms Cl 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 12.4138 12.4138 12.4138 | ||
+ | &END CELL | ||
+ | & | ||
+ | Na 1.0978482003279533E+01 | ||
+ | Cl 1.3489457703231567E+01 | ||
+ | O 1.1753544421905696E+01 | ||
+ | H 1.2340708249225194E+01 | ||
+ | H 1.1333172679938164E+01 | ||
+ | O 1.1014668880096623E+01 | ||
+ | H 1.0569187724590568E+01 | ||
+ | H 1.1898462021703027E+01 | ||
+ | O 1.2689782744905673E+00 | ||
+ | H 1.6331787505516266E+00 | ||
+ | H 2.0695006552397186E+00 | ||
+ | O 1.4178648518519008E+01 | ||
+ | H 1.4017865457100729E+01 | ||
+ | H 1.3483940372104527E+01 | ||
+ | O 1.1452264597040871E+01 | ||
+ | H 1.1967066565244300E+01 | ||
+ | H 1.0557245919373200E+01 | ||
+ | O 5.4034513877480865E+00 | ||
+ | H 4.5483481626988249E+00 | ||
+ | H 5.8745595810397493E+00 | ||
+ | O 1.0057227115948024E+01 | ||
+ | H 9.2698383115214416E+00 | ||
+ | H 9.7419675944524666E+00 | ||
+ | O 8.8677965379732058E+00 | ||
+ | H 8.0047959048088178E+00 | ||
+ | H 8.9279753280405316E+00 | ||
+ | O 3.4080063685919972E+00 | ||
+ | H 4.2321572059400339E+00 | ||
+ | H 2.8950992358414052E+00 | ||
+ | O 3.2104267444392396E+00 | ||
+ | H 2.7530338415002489E+00 | ||
+ | H 2.4556531455595496E+00 | ||
+ | O 4.0963537625725674E+00 | ||
+ | H 3.3568409082389805E+00 | ||
+ | H 4.3609077527930795E+00 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 1.1676278913686788E+01 | ||
+ | H 1.2587464831334719E+01 | ||
+ | H 1.1591655936254574E+01 | ||
+ | O 1.4061976353495059E+01 | ||
+ | H 1.3450288603772332E+01 | ||
+ | H 1.4189484851779527E+01 | ||
+ | O 4.0459889100093029E+00 | ||
+ | H 3.5401823659550020E+00 | ||
+ | H 4.3061858864345899E+00 | ||
+ | O 5.3942555383779709E+00 | ||
+ | H 4.5696452524535074E+00 | ||
+ | H 5.8041847517531799E+00 | ||
+ | O 1.1083204000766642E+01 | ||
+ | H 1.0766380933295238E+01 | ||
+ | H 1.0301075722148791E+01 | ||
+ | O 8.0791998553974889E+00 | ||
+ | H 7.6759201146623637E+00 | ||
+ | H 7.7374893085203249E+00 | ||
+ | O 9.0599466123812089E+00 | ||
+ | H 8.1731340512894715E+00 | ||
+ | H 9.3354403117752280E+00 | ||
+ | O 7.3128194079715705E+00 | ||
+ | H 8.0618288813246686E+00 | ||
+ | H 7.2561941364348446E+00 | ||
+ | O 7.9081332415871142E+00 | ||
+ | H 7.9296786531697769E+00 | ||
+ | H 8.8258690050704462E+00 | ||
+ | O 3.0343124639160681E+00 | ||
+ | H 3.6229508004737765E+00 | ||
+ | H 2.4430790352456935E+00 | ||
+ | O 6.1403349808958954E+00 | ||
+ | H 6.8199298055993873E+00 | ||
+ | H 5.4136904105251489E+00 | ||
+ | O 1.1818413215892830E+01 | ||
+ | H 1.1984376256547076E+01 | ||
+ | H 1.1359766709069046E+01 | ||
+ | O 2.0056876408425651E+01 | ||
+ | H 2.0914912760107462E+01 | ||
+ | H 1.9453366228760853E+01 | ||
+ | O 1.4255904314186182E+01 | ||
+ | H 1.3805349503679688E+01 | ||
+ | H 1.3569123093943860E+01 | ||
+ | O 7.6086778925713991E+00 | ||
+ | H 6.7781094300338305E+00 | ||
+ | H 7.3607191780882069E+00 | ||
+ | O 1.2020909502195277E+01 | ||
+ | H 1.1610474491815115E+01 | ||
+ | H 1.2553354307793303E+01 | ||
+ | O 1.6125272725360077E+01 | ||
+ | H 1.5358446740855484E+01 | ||
+ | H 1.6448807629032782E+01 | ||
+ | O 2.3784433487149315E+00 | ||
+ | H 2.1625304504587910E+00 | ||
+ | H 2.0943392125095457E+00 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 6.2324420266564085E+00 | ||
+ | H 5.5245049044418595E+00 | ||
+ | H 6.9326197318002958E+00 | ||
+ | O 4.7056900888016964E+00 | ||
+ | H 3.8419378351717626E+00 | ||
+ | H 4.3556294121150945E+00 | ||
+ | O 7.9052074989079832E+00 | ||
+ | H 7.8329518120522037E+00 | ||
+ | H 7.1525080724220409E+00 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 1.7533809170986110E+01 | ||
+ | H 1.6717092384419313E+01 | ||
+ | H 1.7543220685207306E+01 | ||
+ | O 9.5953872749122588E+00 | ||
+ | H 1.0238607616030258E+01 | ||
+ | H 9.9642126418558927E+00 | ||
+ | O 8.7359549409803368E+00 | ||
+ | H 8.0301244117232340E+00 | ||
+ | H 8.4028868462495421E+00 | ||
+ | O 1.1342387483264285E+00 | ||
+ | H 1.1431529635020097E+00 | ||
+ | H 1.8795654384061717E+00 | ||
+ | O 4.3425048054329363E+00 | ||
+ | H 4.9653001666371264E+00 | ||
+ | H 3.4795887915173225E+00 | ||
+ | O 6.1470830049255065E+00 | ||
+ | H 6.5254072780528931E+00 | ||
+ | H 6.1233735619293537E+00 | ||
+ | O 6.6165176287786709E+00 | ||
+ | H 5.9988949867397610E+00 | ||
+ | H 6.1011758707194499E+00 | ||
+ | O 8.7448930318205207E+00 | ||
+ | H 9.6172437182814239E+00 | ||
+ | H 8.5879634837153418E+00 | ||
+ | O 9.5857210543430735E+00 | ||
+ | H 8.7011778178526846E+00 | ||
+ | H 9.8328305198610977E+00 | ||
+ | O 7.1655754815424828E+00 | ||
+ | H 6.9362457515784772E+00 | ||
+ | H 7.6766494125251219E+00 | ||
+ | O 4.8297972570762884E+00 | ||
+ | H 5.2224983419581656E+00 | ||
+ | H 3.8202638973321665E+00 | ||
+ | O 6.1141281181639009E+00 | ||
+ | H 6.6741010314616558E+00 | ||
+ | H 5.1417813696946197E+00 | ||
+ | O 1.2422237951227883E+01 | ||
+ | H 1.2774907114847005E+01 | ||
+ | H 1.2383980110238154E+01 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 9.0552712375692934E+00 | ||
+ | H 8.3516076276067128E+00 | ||
+ | H 8.6528091280456980E+00 | ||
+ | O 4.5813760239127364E+00 | ||
+ | H 5.3727323765311770E+00 | ||
+ | H 4.6395747674616947E+00 | ||
+ | O 1.2947678437786887E+00 | ||
+ | H 3.1428367266724405E-01 | ||
+ | H 1.4651549989733721E+00 | ||
+ | O 2.2801010341157997E+00 | ||
+ | H 2.0734054267726179E+00 | ||
+ | H 2.5231047554518509E+00 | ||
+ | O 3.7181632387798422E+00 | ||
+ | H 4.6221675287950585E+00 | ||
+ | H 3.2943497598348452E+00 | ||
+ | O 8.8760226994556335E-01 | ||
+ | H 6.5645671723934040E-01 | ||
+ | H 5.8843124393715890E-02 | ||
+ | O 1.1597624822673641E+01 | ||
+ | H 1.2296467925610532E+01 | ||
+ | H 1.0851674042026399E+01 | ||
+ | O 1.3687809934453169E+01 | ||
+ | H 1.4539114519746876E+01 | ||
+ | H 1.3943283510045202E+01 | ||
+ | O | ||
+ | H | ||
+ | H | ||
+ | O 5.9282480309534415E+00 | ||
+ | H 6.4216163069448253E+00 | ||
+ | H 5.5064601702213665E+00 | ||
+ | O 1.3855624950094682E-02 | ||
+ | H | ||
+ | H 1.6576784524421465E-01 | ||
+ | O 1.4501812945221763E+01 | ||
+ | H 1.3706746681864210E+01 | ||
+ | H 1.5269466984949403E+01 | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | ATOMS 1 2 | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | &END COLVAR | ||
+ | & | ||
+ | CONNECTIVITY GENERATE | ||
+ | & | ||
+ | BONDLENGTH_MAX 7 | ||
+ | &END | ||
+ | &END | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | </ |