Dear Ambers,
I'm doing standard MD simulations on HIV protease (as many of you might know
;) and I observe angular oscillations (that might damp after some
nanoseconds).
My protocol involves minimization of water and hydrogens first, then
minimization of the whole system (no restraints), then heatup phase 50ps (no
restraints).
Not so important:
Are there any obvious improvements that can be suggested for minimization?
Does anybody have experienced for example that its better to relax
side-chains before relaxing the whole system including backbone or something
like this.
Important:
Now I want to use restraints during heatup to guide the molecule to
equilibrium and release it there.
My idea would be to use phi psi backbone torsional restraints. Is this ok or
is there something wrong with this idea?
I want to gradually reduce the restraints during 50ps heatup.
What initial force constant should I use?
Is 50 ps enough for such a procedure?
Should I use a different type of restraint?
Thanks for any suggestions
Regards,
Oliver
--
Oliver Kuhn, Department of Bioinformatics,
Center for Medical Biotechnology, University of Duisburg-Essen,
Universitätsstr. 1-5, 45141 Essen, Germany
phone +49 201 183-3121, oliver.kuhn.uni-due.de
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Received on Tue May 31 2011 - 05:00:02 PDT
