[gmx-users] Gromacs 3.3.1. and 3.3.3

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 9 09:27:28 CEST 2008


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.



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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