Editing GROMACS files for the TIP4P/2005 model

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The following are links to the files for the [[TIP4P/2005]] model of [[water]] for use in the [[GROMACS]] computer [[Materials modelling and computer simulation codes |simulation package]]. These files are located on the web pages of the [http://catalan.quim.ucm.es/ Carlos Vega Statistical Thermodynamics of Molecular Fluids Group]:
The following is a topology file for the [[TIP4P/2005]] model of [[water]] for use in the [[GROMACS]] computer simulation package. The best way to use this file is to click on the edit tab at the top of this page, and then cut and paste the relevant section in the edit window to the file topol.top
 
 
[ defaults ]
; nbfunc        comb-rule      gen-pairs      fudgeLJ fudgeQQ
  1            2              no              1.0    1.0
 
[atomtypes]
;name    mass      charge  ptype    sigma        epsilon
IW    0            0.000      D  0.0          0.0
OWT4  15.99940      0.000      A  0.31589      0.77486
HW    1.00800      0.000      A  0.00000E+00  0.00000E+00
 
 
 
[moleculetype]
; name nrexcl
water 1
 
[atoms]
; nr type resnr residu atom cgnr charge
1    OWT4 1    water  OW1  1    0          15.994
2    HW  1    water  HW2  1    0.5564    1.008
3    HW  1    water  HW3  1    0.5564    1.008
4    IW  1    water  MW4  1    -1.1128    0.0
 
[constraints]
;i j funct doh  dhh
1      2      1      0.09572
1      3      1      0.09572
2      3      1      0.15139
 
[exclusions]
1      2      3      4
2      1      2      3
3      1      2      4
4      1      2      3
 
 
; The position of the dummy is computed as follows:
;
;              O
;
;              D
;
;      H              H
;
; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
;        0.015 nm      / [ cos (52.26 deg)    * 0.09572 nm    ]
 
; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
 
 
[dummies3]
; Dummy from                    funct  a              b
4      1      2      3      1      0.13193828      0.13193828
 
 
[system]
water TIP4P/2005
 
[molecules]
water 1
 


*[http://catalan.quim.ucm.es/gromacs/conf.g96 conf.g96] the coordinate file in [[GROMOS | GROMOS-96]] format
*[http://catalan.quim.ucm.es/gromacs/topol.top topol.top] the topology file
*[http://catalan.quim.ucm.es/gromacs/grompp.mdp grompp.mdp] the input file with the following simulation parameters
** 360 water molecules
** a [[temperature]] of 298 K
** a [[pressure]] of 1 bar
** 8,000,000 [[molecular dynamics]] [[time step]]s
** Van der Waals: 8.5Å cut-off with long range corrections
** [[Electrostatics]]: 8.5Å cut-off with [[Ewald sum]] for the long-range corrections
** [[Nosé-Hoover thermostat]]
** [[Parrinello-Rahman barostat]]


[[category: models]]
[[category: models]]
[[category: water]]
[[category: water]]
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