[gmx-developers] simulation in methanol

[David van der Spoel]

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

> Ranjit
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Ranjit Sudhakar Ranbhor
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Scholar
> Biotechnology Centre
> Indian Institute of Technology-Bombay
> Powai, Mumbai-400 076.
> India.
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> Cell: 91-9820879770
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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