[gmx-users] size of the system

V.V. Chaban vvchaban at gmail.com
Tue Mar 11 16:26:25 CET 2008

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..."

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.


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