[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:
> 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.
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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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