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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>I am also starting to wonder now if you might have other problems.<br>Have you checked if there aren't very strong volume fluctuations?<br><br>Could you mail your mdp pressure coupling parameters?<br><br>Berk.<br></div><br><br><hr id="stopSpelling">> Date: Thu, 27 Mar 2008 15:16:39 +0100<br>> From: reich@mpikg.mpg.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling<br>> <br>> Hi Berk,<br>> <br>> I reran my simulations with the settings you suggested. Unfortunately most<br>> of them crashed. In some of them I received the original error message:<br>> <br>> Source code file: ns.c, line: 313<br>> <br>> Fatal error:<br>> Could not correct too skewed box<br>> <br>> I did not, however, receive this message from all runs. In some cases<br>> conformations were written out for a few steps shortly before the run<br>> crashed, but the simulation process was killed before any error could be<br>> written out. The log-files no proper ending in these cases. Is there any<br>> way to get the error message before the simulation process is killed?<br>> <br>> In one particular simulation the end of the log-file looked like this:<br>> <br>> Correcting invalid box:<br>> old box (3x3):<br>> old box[ 0]={ 5.62033e+00, 0.00000e+00, 0.00000e+00}<br>> old box[ 1]={ 2.79637e+00, 5.26160e+00, 0.00000e+00}<br>> old box[ 2]={-2.81298e+00, -3.13776e-03, 4.54280e+00}<br>> new box (3x3):<br>> new box[ 0]={ 5.62033e+00, 0.00000e+00, 0.00000e+00}<br>> new box[ 1]={ 2.79637e+00, 5.26160e+00, 0.00000e+00}<br>> new box[ 2]={ 2.80735e+00, -3.13776e-03, 4.54280e+00}<br>> <br>> t = 34154.008 ps: Water molecule starting at atom 1615 can not be settled.<br>> Check for bad cont<br>> <br>> <br>> I am not sure whether there is another problem with this simulation<br>> causing the crash. But since the crash occurred directly after the<br>> correction of the box I thought I should report this as well.<br>> <br>> <br>> Best<br>> <br>> Luther<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<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><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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