Yes, you are correct. I am also planning to change mass of side chains of a
protein + water mass, and change mass of the entire system. These two
procedures will have some impact on the time steps. I have to try it and
see.
On Tue, May 13, 2014 at 10:31 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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.
> > > _______________________________________________
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> > > 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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>
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Manikanthan Bhavaraju
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Received on Tue May 13 2014 - 09:00:04 PDT
