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.
________________________________________________________________________
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
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