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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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