GROMACS topology file for the TIP4P/Ice model

The following is a topology file for the TIP4P/Ice 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   0.31668       0.88211
 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 0.5897 1.008 3 HW 1 water HW3 1 0.5897 1.008 4 IW 1 water MW4 1 -1.1794 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 3 4 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 0.13458 0.13458

[system] water TIP4P/Ice

[molecules] water 1