[gmx-developers] simulation in methanol

[Bert de Groot]

David van der Spoel wrote:
> 
> On Fri, 2003-01-24 at 14:04, Ranjit Sudhakar Ranbhor wrote:
> > Hi
> >         While I was trying to do simulation of a peptide in methanol
> > i am facing the following problem;
> >         With genbox, i could solvate the peptide with methanol, but it is
> > not getting registered in top file. Subsequently when i do energy
> > minimisation, with the solvated file, the output .gro file is found to be
> > getting solvated with water, instead of methanol. What could be the
> > problem, and How can it be rectified?
> 
> edit the top file manually.
> check chpater 5 in manual
> 


you're running with a water topology instead of methanol. Probably got some warnings 
about inconsistent filenames in grompp??

the top file should look something like this:


#include "ffgmx.itp"
#include "protein.itp"
#include "methanol.itp"

[ system ]
; name
protein in methanol

[ molecules ]
; name  number
Protein      1
methanol  1757


--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________