[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations?

[unitALX]

Hehe that is a good point!
Indeed, he says that multiple time stepping is a better compromise on
increasing speed. However, he says the NAMD multiple step scheme uses 4fs
for long range electrostatics, while using 1fs for bonded interactions. So
actually, the theoretical root of the disagreement seems to be on the
validity of using length constraints for all bonds. The gist of what he was
saying is that moving to a larger global timestep could cause you to miss
interactions, effectively skipping over small local minima, and deviate
from sampling the "real" hypersurface. He seemed OK with fixing the length
of heavy-atom to hydrogen bonds and doing production at 2fs, but not fixing
heavy-to-heavy bond lengths. Virtual sites + global 4fs seems taboo.

For the same protein, I have a workflow using LINCS all-bonds @ 2fs for
equilibration and production, and a workflow using LINCS all-bonds + vsite
aromatics @ 4fs for equilibration and production. What parameters should I
show for comparison?


On Tue, Feb 11, 2014 at 3:00 PM, Szilárd Páll-2 [via GROMACS] <
ml-node+s5086n5014465h37 at n6.nabble.com> wrote:

> On Tue, Feb 11, 2014 at 12:11 PM, unitALX <[hidden email]<http://user/SendEmail.jtp?type=node&node=5014465&i=0>>
> wrote:
>
> > Helllo all!
> >
> > In my general situation, I have a batch of homology models that I would
> like
> > to assess for stability by molecular dynamics.
> >
> > I am working with a postdoc in my lab who was extensive experience with
> > NAMD, but does not use GROMACS. We have been developing protocol for
> these
> > MD simulations, but we had some different views on equilibration and
> > production.
> >
> > Equlibration
> > My friend is recommending that I do equilibration for 500ps @ 1fs with
> no
> > constraints. I have no real objection to that, but he made it seem like
> the
> > results might be quite different than an equilibration for 200ps @ 2fs
> with
> > LINCS all-bonds. Would it make a critical difference?
> >
> > Production
> > I was excited by the performance possible with LINCS all-bonds, -vsite
> > aromatics @ 4fs, but my friend looks at 4fs with disgust.
>
> I would you mind asking your friend whether multiple time stepping
> disgusts him too? :)
>
> --
> Szilárd
>
> > I responded with
> > arguments from the GROMACS 4 paper, and a paper called "Improving
> efficiency
> > of large time-scale molecular dynamics simulations of hydrogen-rich
> systems"
> > re: the relationship between the period of the fastest vibration and
> largest
> > allowable timestep, but he seems quite convinced that for publication,
> only
> > 1fs and possibly 2fs production runs (preferably without barostat and
> > thermostat??) are acceptable. The suggestion to drop the barostat and
> > thermostat for production follows the philosophy that if your
> minimization
> > and equilibration is properly done, then the system should be stable in
> > production without pressure & temperature control. I'm having a hard
> time
> > finding better literature "justifications" for usage of LINCS all-bonds
> @
> > 2fs, and certainly for -vsites @ 4fs; P&T control seems quite standard
> in
> > publications using GROMACS.  Can you suggest any papers or calculations
> I
> > can do to show the validity of these options?
> >
> > --
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