[gmx-users] Gromacs 3.3.1. and 3.3.3

[Berk Hess]

Hi,

I agree with Tsjerk, but his mail might have not answered your question exaclty.

In general one should not switch between major revisions in one project.
But there should be nearly no differences in simulation results between
minor revisions. If there are differences this means that a bug was fixed
and you should be using the newer revision anyhow.
So I would suggest switching to 3.3.3.

Berk


> Date: Thu, 9 Oct 2008 09:27:28 +0200
> From: tsjerkw at gmail.com
> To: minnale_gnos at rediffmail.com; gmx-users at gromacs.org
> Subject: Re: [gmx-users] Gromacs 3.3.1. and 3.3.3
> CC: 
> 
> Minnale,
> 
> Hmm, I thought I recalled answering a similar question just recently.
> But mind you that doing statistics on MD, unless the results are very
> obvious, you have to be as careful and consistent as can be. That
> means that you should avoid trying to compare things which are
> performed under different conditions, and program versions is one of
> them. In fact, I believe there are some differences between 3.3.1 and
> 3.3.3 which can be expected to affect the results, so in a comparison,
> you wouldn't have any means of assessing the source of differences
> observed. Besides that, having only single simulations makes most
> comparisons tricky anyway. You should really try to rerun the
> simulations to obtain an estimate of the natural range of observables
> you can expect. In that case, you could either try randomizing program
> versions or stick with one.
> To cut it short, don't try to make any comparisons beyond the obvious:
> you don't have enough statistics and you can probably not exclude an
> effect of running with different versions of gromacs.
> 
> As a side note, when performing simulations to compare effects of
> simulation parameters, mutations, whatever, it is more important to
> design and perform a set of simulations in a consistent manner than to
> have the parameters, force field etc. perfectly apt for reproducing
> reality. Of course the latter will help and will improve statements of
> quantitative nature.
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On Thu, Oct 9, 2008 at 9:03 AM, minnale <minnale_gnos at rediffmail.com> wrote:
> >
> > Hi Users,
> > I have run protein system till 25ns in gromacs version 3.3.1 in dual
> > processor system. Now I want to run new systems in cluster with gromacs
> > version 3.3.3, in two cases the  protein system is same but difference in
> > few residues, If run new system in cluster compare the results with already
> > ran protein system, will it make any difference?
> >
> >
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> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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