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
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> 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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Received on Tue May 13 2014 - 08:30:03 PDT
