<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
If mdrun hangs -maxh won't help.<br>You can kill mdrun using the kill command.<br>But since mdrun catches signals, you might need kill -9 (the 'KILL' signal).<br><br>Berk<br><br>> Date: Mon, 14 Sep 2009 10:56:43 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Limit mdrun runtime<br>> <br>> <br>> <br>> Jack Shultz wrote:<br>> > Hello,<br>> > <br>> > I have developed a workflow for prepping structures. One problem I have <br>> > is sometimes it gets hung up on mdrun. Are there any mdrun parameters we <br>> > can use to kill this process if it runs too long? The parameters we are <br>> > using should not run over 5 minutes. I have not figured out how to do <br>> > this with my script, but I guess there may be a way using SIGALRM.<br>> > <br>> <br>> mdrun -maxh<br>> <br>> -Justin<br>> <br>> > -- <br>> > Jack<br>> > <br>> > http://drugdiscoveryathome.com<br>> > http://hydrogenathome.org<br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.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>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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>
</html>