[gmx-users] MD simulations of dipeptide in crystal lattice
David van der Spoel
spoel at xray.bmc.uu.se
Sun May 7 08:51:06 CEST 2006
List User wrote:
> I would like to perform MD simulations of a small molecule (dipeptide)
> in a crystal lattice, where I believe that lattice contacts may be
> important for the structure and dynamics. I assume this can be done
> by simulating one or more unit cells and applying periodic boundary
> conditions, but I don't find any examples of this. Is there a
> tutorial which illustrates how crystal symmetry can be included in
> these simulations? I would appreciate any help, pointers, or advice
> that you can provide.
just make a crystallographic unitcell and use that as starting
structure. initially you should be careful with pressure coupling.
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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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