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
Received on Tue May 13 2014 - 08:30:04 PDT
