Dr. Aragon,
Thanks for providing your valuable insights.
mani
On Tue, May 13, 2014 at 12:35 PM, Sergio R Aragon <aragons.sfsu.edu> wrote:
> Hello Mani,
>
> I'll add my two cents worth to this discussion. Diffusion coefficients,
> when you are in the hydrodynamic regime are mass independent. For
> simulations of molecules larger than water to the microsecond time scale,
> you are in the hydrodynamic regime. Thus changing the masses will not gain
> you anything at all. Most dynamics, even that of smallish molecules
> translate in the hydrodynamic mode (and to calculate it you must use slip
> boundary conditions in classical hydrodynamics), whenever the solute is
> simply larger than any void volumes in the solvent. This certainly covers
> your molecules of interest in water (because you are in water, you would
> need the hydrodynamic stick boundary conditions to calculate transport in
> classical hydrodynamics). The underlying reason for this is that the
> motion is overdamped, so the accelerations average to zero and thus mass
> disappears from the picture.
>
> When you use a water model such as TIP3P, the viscosity is already about a
> factor of two too small and dynamics is already accelerated. This is a
> defect of the water model, but it comes in handy in improving the speed of
> simulations when global solute dynamics is not intended to be extracted
> from the trajectory; only local, nonhydrodynamic dynamics is correct in
> that water model.
>
> One possible way to reach very long simulation times is to try Brownian
> dynamics simulations. Another is to generate a coarse grained model of
> your system so that you have fewer effective atoms to move. To preserve
> chemical accuracy, you would need to train your models on shorter atomistic
> simulations.
>
> A third method is the brute force method. We published the first long
> scale simulation (.32 microseconds) of an antibody (Trastuzumab) using
> ff99SB in TIP3P in 2010. The work took two years of computation because we
> didn't have GPUs at that time. It was still worth it. People are doing
> microsecond long simulations on GPUs now, so you may resign yourself to
> spending the time doing it right.
>
> Cheers,
>
> Sergio Aragon
> Professor of Chemistry
> San Francisco State University
>
> -----Original Message-----
> From: Manikanthan Bhavaraju [mailto:manikanthanbhavaraju.gmail.com]
> Sent: Tuesday, May 13, 2014 10:05 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Scaling of atomic mass of water molecules
>
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Manikanthan Bhavaraju
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>
>
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Received on Tue May 13 2014 - 11:00:09 PDT
