<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
<br><br>> Date: Thu, 25 Jun 2009 18:39:53 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Re: Re: problems with some calculated trajectories<br>> <br>> Bernhard Knapp wrote:<br>> > 1) trjconv with the "-pbc nojump" option does not help - it removes most <br>> <br>> If I understand correctly, -pbc nojump will help when the relevant atoms <br>> are part of the same [moleculetype]. One fragment in each of your two <br>> examples is apparently the same four-strand sheet with helix wrapped <br>> around it. This suggests to me that you might have several chains, each <br>> as a different [moleculetype] and your observations are actually what <br>> you should expect. If so, -pbc cluster is the kind of thing you should <br>> be using.<br>> <br><br>You did not understand correctly :)<br>-pbc nojump removes periodic jumps of atoms, it does not now about molecules.<br>The effect is that no periodic jumps occur from the reference structure<br>(either tpr or first frame). This means, for instance, that protein complexes<br>will stay intact and that water will diffuse out of the box in visualization.<br><br>Berk<br><br>> In any case, a description of the composition of your system and copies <br>> of a series of commands that reproduces your result would always have <br>> been appropriate :-)<br>> <br>> Mark<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 />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
</html>