Editing GROMACS files for the TIP4P/2005 model

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



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