[gmx-users] invacuo simulation

[David van der Spoel]

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? 
> 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
> anwar.m1 at gmail.com
> -----------------------
> 
> 
> 
> -
> 
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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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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