Many thanks for your advice.
Oliver
2011/5/31 Carlos Simmerling <carlos.simmerling.gmail.com>
> I've had poor luck with such simple equilibrations.
> We usually do a series of MD runs, with equilibration of water and all
> built
> atoms first, then restraints on fewer atoms (first all heavy, then backbone
> only) and heating /minimization steps. I don't heat from 0, I have had bad
> experiences and always start MD at 200K or so and heat from there. we only
> use positional restraints.
>
> On Tue, May 31, 2011 at 9:03 AM, Oliver Kuhn <oak.amber.googlemail.com
> >wrote:
>
> > 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).
> >
> > -> That means, I observe oscillations in the sum of angle energies of the
> > complex (see attached plot - 100ps blockwise averages) (in 21 independent
> > simulations)
> >
> > 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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>
--
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 - 12:00:03 PDT
