[EMAIL PROTECTED] 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?
regards
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.
Anwar
----------------------
Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Nacharam
Hyderabad-500 076
INDIA.
Tel: +91-8413-235467,68,69,70 ext 2019
[EMAIL PROTECTED]
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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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