[gmx-users] invacuo simulation
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 4 19:03:40 CEST 2006
anwar at cdfd.org.in wrote:
> Dear gmx users,
> I am working on protein invacuo simulation in different condition like
> considering different box size (0.7, 0.8, 1.0) and also with and without
> pressure coupling. When I am looking at the rmsd and gyration results,
> they are all varying alot for all the simulations.
> The simulation seem to be equilibrated for a certain time and then but
> again they start deviating. I dont have any clue for why the system is
> showing a lot of discrepancies with in different simulations when they
> differ only in the box size. Can some on through some light on it?
pressure coupling does not make sense in vacuum, because there is no
box. If you want to use PBC and a box anyway the size doesn't matter
except that the molecule should not see it's own image.
> Mohd Anwaruddin
> Project Assistant
> C/o DR.H.A.Nagarajaram
> Lab of Computational Biology and Bioinformatics
> Center for DNA Fingerprinting and Diagnostics(CDFD)
> Hyderabad-500 076
> Tel: +91-8413-235467,68,69,70 ext 2019
> anwar.m1 at gmail.com
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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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