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

[Piggot T.]

Hi,

Personally I would also ask your colleague if he could also provide evidence (e.g. published papers) to back up what he is saying to you (i.e. that it is necessary to use a 1 fs timestep with an NVE ensemble to achieve acceptable results). This way, you can make an informed decision based upon the available evidence you can find, rather than simply upon one persons view point. I would suggest the he will find it difficult to come up with such evidence for your case of a straight forward MD simulation.

You should also remember that you are the one that will need to be able to defend (to an examiner or reviewer) what you have done and why. Simply "because the postdoc told me it was the correct thing to do" will (unfortunately) not be good enough!

Cheers

Tom
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Szilárd Páll [pall.szilard at gmail.com]
Sent: 11 February 2014 13:33
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] "Justifying" 4fs production runs after 1fs     equilibrations?

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? :)

--
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?
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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