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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Received on Tue May 13 2014 - 08:00:03 PDT
