<DIV>Hi, David, </DIV>
<DIV>Do you know what is the reason that atoms explod? </DIV>
<DIV>Is it because that I did not include bond force and constraints or other wrong parameters?</DIV>
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<DIV>thanks!</DIV>
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<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">
<DIV><B><I>David <spoel@xray.bmc.uu.se></I></B> wrote:
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">On Thu, 2003-08-28 at 23:07, Albert Sun wrote:<BR>> Dear David van der Spoel,<BR>> I am testing a simple case, and prepared top and gro files as<BR>> attached, when I ran EM.mdp and 9atom.mdp, and see ngmx, it has the<BR>> error: segmentation fault.<BR>> (em.mdp file is attached in another email)<BR>> Could you help me to have a look?<BR><BR>I see a system of 9 atoms in a plane which explodes after roughly 100 fs<BR>(I decreased nstxout to 5 to see it).<BR><BR>If you do not see that, then I suggest you try to run it on a Linux or<BR>Unix box first. By the way, ngmx won't work on a DOS anyway.<BR><BR><BR>-- <BR>Groeten, David.<BR>________________________________________________________________________<BR>Dr. David van der Spoel, Dept. of Cell and Molecular Biology<BR>Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>phone: 46 18 471 4205 fax: 46 18 511
755<BR>spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel<BR>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<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.</BLOCKQUOTE></DIV>
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