[gmx-users] RE: how many water molecule used to run MD?

Vitaly Chaban chaban at univer.kharkov.ua
Mon Sep 22 09:22:49 CEST 2008

> If I want to include more than 1000 TIP4P or TIP5P water molecules in
> my MD system, how could I construct the TIP4P.gro and TIP5P.gro files
> ?

genconf -f onewater.gro -o box.gro -nbox N N N,

where onewater.gro contains the coordinates of one water molecule and
N - is a number of water molecules per cubic box side.

genbox -cp onewater.gro -cs onewater.gro -o box.gro -box N N N -maxsol

where M is a desired number of molecules in the box, N - is each side
length in nanometers.

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698

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