<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>I think not.<br>If mdrun could not read the table files it would complain about that.<br>Have a look in your md.log file to see what mdrun did.<br><br>At which step did it segfault?<br>Do you have the energies at step 0?<br>If so, do they look reasonable?<br>Did you energy minimize your system?<br><br>Berk.<br><br></div><br><hr id="stopSpelling">> Date: Tue, 27 May 2008 21:51:11 +0800<br>> From: catfish.hku@gmail.com<br>> To: gmx3@hotmail.com; gmx-users@gromacs.org<br>> Subject: RE: [gmx-users] How to use tabulated potentials to do coarse grained simulation?("Segmentation fault" when running mdrun.)<br>> CC: <br>> <br>> Dear Berk and all GMX users,<br>> <br>> Thanks a lot for your instructions. I have corrected my errors and are<br>> using h, h'' for my foces.<br>> C12 is set to 1 correspondingly.<br>> However I still get "Segmentation fault" when running mdrun.<br>> the version of GMX that I am using is 3.3 and I also tried 3.3.3<br>> Are there still anything wrong with my setting files?<br>> Need I specify energy groups in mdp file?<br>> <br>> Thanks a lot<br>> <br>> > Message: 4<br>> > Date: Mon, 26 May 2008 15:51:43 +0200<br>> > From: Berk Hess <gmx3@hotmail.com><br>> > Subject: RE: [gmx-users] How to use tabulated potentials to do coarse<br>> > grained simulation?<br>> > To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> > Message-ID: <BLU134-W4011463649FCAAE70C23AC8EC20@phx.gbl><br>> > Content-Type: text/plain; charset="iso-8859-1"<br>> ><br>> > Hi,<br>> ><br>> > You potential is zero, since all your force-field parameters are zero.<br>> > Your should use g or h (not f, since this is the electrostatics function)<br>> > and set c6 or c12 (when using g or h) to 1.<br>> > See eq. 6.21 in the manual.<br>> ><br>> > Berk.<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>
</html>