[gmx-users] size of the system

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 11 17:40:29 CET 2008

Quoting "V.V. Chaban" <vvchaban at gmail.com>:

> Dear Colleagues,
> I've got a novice question as for GROMACS. For example, I need a system
> of 500 water molecules. Initially, I've spc216.pdb. Then I try:
> pdb2gmx -f spc216.pdb -o conf.pdb
> editconf -f conf.pdb -o box.pdb -d 0.7
> genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top
> The utility outputs:
> "......
> solvent configuration contains 648 atoms in..."

...it is always best to include the whole output when asking for free help :)

Which version of Gromacs?  How was it compiled?  It is well-documented across
this list (and on the Downloads site, if I recall) that the gcc 4.1.x compilers
produce a broken product.

Your approach seems reasonable, by the way.  Do some back-of-the-envelope
calculations to determine the appropriate box size to obtain 500 water
molecules.  It looks like your initial approach might work with a functioning


> and hangs up.
> Where am I wrong? And how can one obtain the system of the desires
> quantity of molecules using GROMACS utilities?
> Thanks in advance.
> --
> Vitaly
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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