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 <[EMAIL PROTECTED]> 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? > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
