[gmx-users] Strange output with Genbox

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 13 14:26:48 CET 2008

Jens Pohl wrote:
> Hello!
> I try to simulate a modified protein in a water-box. When I use genbox and have a look on the output-file then the water molecules are located in between the AA-sequence which results in an "exploding" molecule during the mdrun. I've done it several times from the very beginning, always getting a similar result (distribution of water in the AA sequence varied a bit). 
> Input-sequence (AA):
> Output after genbox:
> Commands used (copied from .bash_history):
> pdb2gmx -f 165_in.pdb -p 165 -o 165 -n 165 -i 165 -q 165_out.pdb
> (used ffG53a6)
> editconf -f 165 -o CbzE_ec.pdb -bt cubic -vol -d 1.0 
> genbox -cp 165_ec.pdb -cs ../Water.gro -o 165_gb.pdb -p 165_gb

What is in ../Water.gro? It should be pure water.

What system are you running on?

> Thank you very much in advance for your suggestions to solve the problem
> Jens
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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