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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>I agree with Tsjerk, but his mail might have not answered your question exaclty.<br><br>In general one should not switch between major revisions in one project.<br>But there should be nearly no differences in simulation results between<br>minor revisions. If there are differences this means that a bug was fixed<br>and you should be using the newer revision anyhow.<br>So I would suggest switching to 3.3.3.<br><br>Berk<br></div><br><br><hr id="stopSpelling">> Date: Thu, 9 Oct 2008 09:27:28 +0200<br>> From: tsjerkw@gmail.com<br>> To: minnale_gnos@rediffmail.com; gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Gromacs 3.3.1. and 3.3.3<br>> CC: <br>> <br>> Minnale,<br>> <br>> Hmm, I thought I recalled answering a similar question just recently.<br>> But mind you that doing statistics on MD, unless the results are very<br>> obvious, you have to be as careful and consistent as can be. That<br>> means that you should avoid trying to compare things which are<br>> performed under different conditions, and program versions is one of<br>> them. In fact, I believe there are some differences between 3.3.1 and<br>> 3.3.3 which can be expected to affect the results, so in a comparison,<br>> you wouldn't have any means of assessing the source of differences<br>> observed. Besides that, having only single simulations makes most<br>> comparisons tricky anyway. You should really try to rerun the<br>> simulations to obtain an estimate of the natural range of observables<br>> you can expect. In that case, you could either try randomizing program<br>> versions or stick with one.<br>> To cut it short, don't try to make any comparisons beyond the obvious:<br>> you don't have enough statistics and you can probably not exclude an<br>> effect of running with different versions of gromacs.<br>> <br>> As a side note, when performing simulations to compare effects of<br>> simulation parameters, mutations, whatever, it is more important to<br>> design and perform a set of simulations in a consistent manner than to<br>> have the parameters, force field etc. perfectly apt for reproducing<br>> reality. Of course the latter will help and will improve statements of<br>> quantitative nature.<br>> <br>> Cheers,<br>> <br>> Tsjerk<br>> <br>> <br>> On Thu, Oct 9, 2008 at 9:03 AM, minnale <minnale_gnos@rediffmail.com> wrote:<br>> ><br>> > Hi Users,<br>> > I have run protein system till 25ns in gromacs version 3.3.1 in dual<br>> > processor system. Now I want to run new systems in cluster with gromacs<br>> > version 3.3.3, in two cases the protein system is same but difference in<br>> > few residues, If run new system in cluster compare the results with already<br>> > ran protein system, will it make any difference?<br>> ><br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> <br>> <br>> <br>> -- <br>> Tsjerk A. Wassenaar, Ph.D.<br>> Junior UD (post-doc)<br>> Biomolecular NMR, Bijvoet Center<br>> Utrecht University<br>> Padualaan 8<br>> 3584 CH Utrecht<br>> The Netherlands<br>> P: +31-30-2539931<br>> F: +31-30-2537623<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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