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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Thu, 6 Mar 2008 13:57:31 +0100<br>> From: stephane.teletchea@jouy.inra.fr<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling<br>> <br>> Berk Hess a écrit :<br>> > Hi,<br>> > <br>> > I now realized that my fix what completely incorrect.<br>> > I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5.<br>> > But my mistake means that is now given an error when the off diagonal<br>> > element is relatively more than 1 instead of more than 0.5.<br>> > This is a far too weak check.<br>> > So I would not expect any fatal errors any more with this incorrect check.<br>> > Therefore I don't understand why you still get errors.<br>> > <br>> > Could you try changing BOX_MARGIN to 0.5005, as it currently is in <br>> > version 4.0?<br>> > <br>> > Berk. <br>> <br>> We thus need a hot fix for 3.3.3?<br><br>A too weak check does, by itself, not cause problems.<br>It does mean that the check is useless, but Gromacs<br>by itself never generates incorrect boxes.<br><br>The problem with the check is still there, but it only<br>seem to occur very rarely.<br>I'll fix it properly in the CVS 3.3 patches branch.<br><br>> <br>> To Luther:<br>> Do you have by any hazard<br>> constraints = all-bonds<br>> <br>> if so, could you check if the run has the error with h-bonds?<br>> <br>> In my case that solved the issued with the error message. I suspect a <br>> rounding problem but i have not figured out it yet (not really searched <br>> for, btw).<br><br>I don't think this should have anything to do with the problem directly.<br>Indirectly it could help, but only when the system is unstable.<br><br>Berk.<br><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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