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

Szilárd Páll pall.szilard at gmail.com
Tue Feb 11 14:33:29 CET 2014

On Tue, Feb 11, 2014 at 12:11 PM, unitALX <alec.zander at gmail.com> 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? :)


> 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?
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html
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