one thing to keep in mind as you do this is that you need to think about
which water model you will be using. commonly used models in Amber are
rigid, so the impact on possible time steps will likely not be dramatic.
also, changing the water mass won't (by itself) change the masses of other
solute atoms, and Amber doesn't do the time steps for the water different
from solute. This means you probably won't be able to take longer time
steps in your MD just because you've changed the water mass. others here
can comment on methods to repartition masses of solute atoms, which is
possible in Amber and may help you.
On Tue, May 13, 2014 at 11:16 AM, Manikanthan Bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Yes, I have not found this kind of work to be done in amber community (I
> might be wrong). Since protein aggregation happens in the time scale of
> micro seconds. I want to see whether sort of approach will effect the
> sampling or not.
>
> mani
>
>
> On Tue, May 13, 2014 at 9:59 AM, Brian Radak <radak004.umn.edu> wrote:
>
> > I don't think this kind of "trick" has been used in AMBER very often, if
> at
> > all. Most classical static quantities of interest in the canonical
> ensemble
> > are mass invariant, so your plan is likely sound, but I don't have any
> > ideas as to how sampling will be affected. Perhaps that is why it is not
> > done very often?
> >
> > Regards,
> > Brian
> >
> >
> > On Tue, May 13, 2014 at 10:51 AM, Manikanthan Bhavaraju <
> > manikanthanbhavaraju.gmail.com> wrote:
> >
> > > Dear All,
> > >
> > > I am interested to study the mechanism of protein aggregation using an
> > > explicit solvent simulations. As a model system we have taken a
> amyloid
> > > protein ~ 100 residues. Initially, I would like to analyze the affect
> > of
> > > scaling of atomic mass of the water molecules vs. standard simulation
> > > techniques. My assumption is that scaling the atomic mass of the
> solvent
> > > molecules can decrease the viscosity of the system, avoid heating
> > > (performing minimization and production runs), take larger time steps,
> > and
> > > the system to some extent will be able to quickly cross the energy
> > barriers
> > > on the potential energy surface.
> > >
> > > On the other hand, I want to conduct a regular explicit solvent
> > simulation
> > > (minimization, heating, equilibration, and production) and then compare
> > > both the results. Can you anyone give me some suggestions or their
> > expert
> > > opinion on this kind of analysis?
> > >
> > > Thanks,
> > >
> > > mani
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Manikanthan Bhavaraju
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 13 2014 - 09:00:03 PDT
