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<TD><strong><em><SPAN STYLE="font-style: italic;"><span style="font-weight: bold;"></span></SPAN></em></strong>Thank you for the reply. I have some more queries:<br ><br >So if I load Gromacs 3.3.1 on Octane will I gain on the time a bit ? <br >Do you suggest me to update the Gromacs versions on both the systems to Gromacs 3.3.1? <br >For this do I have to remove the older versions ? Will it over write.<br >Can I keep both the versions loaded on the system or will there be a clash ? Do I have to load fftw once again ?<br >Bothering you with too many questions ! Answers for these would help me to decide .<br ><br >Thanks in advance.<br ><br >sharada<br ><br ><br ><br ><strong><em>-- Original Message --</em></strong><br >From: "Mark Abraham" <mark.abraham@anu.edu.au><br >To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br >Date: Thu, 4 Jan 2007 19:32:27 +1100 (EST)<br >Subject: Re: Re: [gmx-users] Difference in the Forcefields and speed...<br ><br >> If I do the MD studies using Gromacs 3.1 and Gromacs 3.3 with differennt<br >> forcefields like ffg43a1 and ffG53a5 respectively in the same simulating<br >> conditions how different would be my results ? or will there be any<br >> difference ?<br ><br >In theory both forcefield models are accurate representations of reality<br >over the domain over which they were parametrized. There's no guarantee<br >that they'd be similar to each other on a given domain, or to reality, and<br >the further you get from their parameterization domain, the worse the<br >chances.<br ><br >Ignoring a handful of bug fixes, gromacs 3.1 and 3.3 should produce<br >similar ensembles, but they cannot be exactly the same.<br ><br >> Is there a difference in the speed of the simulations say if I run them<br >> on SGI Octane R12000 and a Personal computer with 512 RAM Pentium III ?<br >> Incidently Gromacs 3.1 is loaded on Octane and Gromacs 3.3 on Pentium III<br ><br >Yep.<br ><br >> Why I am asking the second question is that the time taken on Octane is<br >> much larger ( around 9 days) compared to the Pentium III (3 days) what may<br >> be the reason ?<br ><br >Probably, the assembly-language optimized inner loops are being used on<br >the PIII, and generic inner loops on the Octane. The vast majority of MD<br >simulation time is spent in these loops, so they are critical to<br >performance. Obviously, native CPU speed is also an issue here too.<br ><br >Mark<br ><br >_______________________________________________<br >gmx-users mailing list gmx-users@gromacs.org<br >http://www.gromacs.org/mailman/listinfo/gmx-users<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 ></TD>
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