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Hi,<br><br>I don't know what the reason for the large LJ14 distance is,<br>but this will be over 3 bonds, not over 1 bond (which I guess the 0.154 is<br>that you mentioned).<br><br>This has nothing to do with the parallelization.<br>I would use 4.0.2, since there are many small issues fixed that were in 4.0.0.<br>In 4.0.0 you communicate twice as many atoms, so 4.0.2 will run faster.<br>I would suggest to run mdrun -rdd 1 and see if you don't get the missing<br>interaction errors anymore.<br><br>Berk<br><br><hr id="stopSpelling">Date: Wed, 19 Nov 2008 14:06:17 +0000<br>From: lastexile7gr@yahoo.de<br>Subject: RE: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew error<br>To: gmx-users@gromacs.org<br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top"><div id="EC_yiv990679034">Hello,<br><br>thank you for all your responses up to now. The thing is getting much more clearer.<br><br>Yet, as far as the distance is concerned, this is a little bit worrying, because I have bonded interactions no more than 0.154 nm away. So a distance more than a whole nm I think that should be very long so as to keep this message to go away. If this has to do with the parallelization, then I might not worry. Yet, physicaly I think that is a very long distance.<br><br>I have to say that the same system worked very nicely with the version 4.0.0 and looking it via ngmx I saw nothing worrying. The properties of my system where reasonable too.<br><br>I insist, because in previous gromacs versions I got similar errors and their cause was due to running on many processors. The run was crashing, yet running it only in two
processors I didn't face such problems. It is also curious because in version 4.0.0 I didn't see such an error. <br><br>The runs I make take a lot of time, so seeing different error messages at random makes the post process even more difficult. The 1nm you propose I think that it is a big distance both for the LJ pairs interactions and of course for the bonded ones. Also I thought that the table extention was a cut-off for the LJ pairs interactions, which in my case is 5 nm.<br><br>The only thing I can think of for now is to run in less processors...<br><br>Thank you, <br>Regards!<br></div></td></tr></tbody></table><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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