<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>I should add, one is an automated submit system, the others manual quing where you set parmeters (the ones that work), and the system is large around 90 120 90 angstrom box with around 170-180,000 atoms. Still, the que output from the manual submission simply sets -nt 6, and the rest of the input as standard defaults.
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Samstag, 15. Juni 2013 um 02:05 Uhr<br/>
<b>Von:</b> "lloyd riggs" <lloyd.riggs@gmx.ch><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Aw: Re: [gmx-users] Re:Problems with extending runs</div>
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<div style="margin: 10.0px 5.0px 5.0px 10.0px;padding: 10.0px 0 10.0px 10.0px;border-left: 2.0px solid rgb(195,217,229);"><b>I have a bizzar problem. I did 21 simulation for 4 ns each. These were equ'd for 4ns prior, then taken from an assembly run over 4ns so between 300 pico and 4ns additional each. A reviewer wants a couple extnded ends added,say like 4 extra ns, which I can only do 1-4 at most due to time limits (they take several days with 4-5 nodes, 8cpu quad core amd) Now I just simply took the end run .mdp files, added these on, generated .tpr file, and a short check to generate a checkpoint .cpt. I ran one on the cluster here in bern, one on a home PC and submitted one to the dutch/euro grid system. The one on the grid in bern works fine, the one on my PC as well (intel 8 core), however it only reaches 75,000 of 20 million time steps necessary in 8 hours, I could never go beyonda 0.0005 time step (well 0.0008 but kept it at the former due to ease of changing file parmeters), any case, when I submit it to the Eu/dutch grid it crashes at at step 5000 with a PME, non-equilibrated error. My question is why does it run on one, the exact same tpr tested, but not the other?</b></div>
<div style="margin: 10.0px 5.0px 5.0px 10.0px;padding: 10.0px 0 10.0px 10.0px;border-left: 2.0px solid rgb(195,217,229);"><b>I looked at versions 4.5.5 my pc, 4.5.7 at unibe and a altered version of 4.5.3 on the dutch/eu grid. Other than that, I can not find a problem, but woundered, as use of an extra que would have helped but most likely not now, as I have a response time.</b> I can not fathom why it would give such large changes however in bonds/angles in one but not the other as the versions are not that different? Was there a large change between these versions, or other possibilities?</div>
<div style="margin: 10.0px 5.0px 5.0px 10.0px;padding: 10.0px 0 10.0px 10.0px;border-left: 2.0px solid rgb(195,217,229);"><b>Stephan Watkins</b></div>
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