[gmx-users] Solvating with glycerol

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 24 09:23:08 CEST 2006

Arneh Babakhani wrote:
> Hello,
> I have a small peptide that I'd like to solvate with glycerol (instead 
> of water).  I couldn't find a .gro and .itp file for glycerol in the top 
> directory.  I was wondering if anyone has such files and would be 
> willing to share them?

> In looking at the other solvent .gro files (i.e. spc216.gro, dmso.gro),  
> each structure file contains many molecules of that solvent.  Is this 
> necessary?  In other words, can the .gro file contain just one molecule, 
> and will genbox work with that?

you save a lot of time by pre-equilibrating the solvent.
> thanks,
> Arneh
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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