Hi Emanuel,<div><br></div><div><div><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="EN-AU" link="blue" vlink="purple"><div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">What kind of compounds are you simulating?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"></span></p></div></div></blockquote><div>~1800 atom protein</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-AU" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">What size of box are you using?</span></p></div></div></blockquote><div>Not sure of specifics, since the tpr file was provided by a collaborator, but it appears to be ~ 7nm in each dimension</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="EN-AU" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Do you run on multiple thread when you run it on your iMac?</span></p></div></div></blockquote><div>No. Compiled with --disable-threads</div><div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="EN-AU" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">How many CPU’s are you using on the cluster?</span></p></div></div></blockquote><div>1. Compiled with --disable-threads</div><meta charset="utf-8"><div><br>
</div><div>I'm not so much interested in diagnosing what caused the LINCS failure as I've spent a lot of time trying that already. I'm more concerned about what is the difference between the two environments that leads to such a failure. That one produces a stable simulation and one so stubbornly refuses to work implies a pretty significant difference.</div>
<div><br></div><div>What can I change to try to identify the cause of this discrepancy?</div><div><br></div><div>Thanks,</div><div>Luke</div></div></div></div>