I taught of lowering the masses by half. However, your explanation makes
sense. I will go through the paper that you have suggested. Thanks for the
information.
mani
On Tue, May 13, 2014 at 11:50 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi
>
> Well, first, tell us if you are going to increase or decrease the masses...
>
> This has a long history in the field, and for the most part, it has
> never worked well.
>
> Basically, there are arguments about lowering masses to increase
> diffusion coefficients. This seems ok, but then all vibrational
> frequencies go up and you need a much short time step to make it work.
> Hence, no gain.
>
> You can increase all masses, and then you get to increase your time
> step. That seems reasonable, but simple stats mech will show you that
> what you have messed up with the velocities. If you are still running at
> the same temperature as before, let's say 300K, that correlates with the
> kinetic energy. So, if your kinetic energy is the same as with regular
> masses, your velocities must have been reduced as the square root of the
> mass change. So, things will move slower, and you loose...
>
> There is something called HMR, hydrogen mass repartitioning. We are
> about to submit a paper on this, but essentially consists of taking
> local chemistry (e.g. CH2RR')
> and increasing the H mass and decreasing the H-partner mass in such a
> way that the 'local' mass has not changed.
>
> This means that the total mass of the system is still the same as before
> the repartitioning, and things are much better from a stat mech point of
> view.
>
> Once you do this, you can push your time step to 4 fs and gain a factor
> of 2x in overall speed.
>
> This is an EXPERT mode... We tested it a lot in amber, with different
> observables, and it work great. Some other people within Amber have also
> tried it and it works for them. Again, things break sometimes, so the
> use does not come with a warranty...
>
>
> Some of these ideas were expressed in "Improving efficiency of large
> time-scale MD simulations in hydrogen rich systems. Feenstra, Hess,
> Berendsen. J Comp Chem 1999"
>
>
> On 5/13/14 10:59 AM, Brian Radak 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
> >>
> >
>
> --
> Dr. Adrian E. Roitberg
>
> Colonel Allan R. and Margaret G. Crow Term Professor.
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Manikanthan Bhavaraju
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Received on Tue May 13 2014 - 10:30:02 PDT
