<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;"><br></div><br><br><br><hr id="stopSpelling">> From: ddubov@ngs.ru<br>> To: gmx-users@gromacs.org<br>> Date: Fri, 16 May 2008 18:20:02 +0700<br>> Subject: [gmx-users] Ordering with trjorder<br>> <br>> Dear gmx_users,<br>> <br>> could you clarify me how the "trjorder" procedure works? <br>> Manual says "For each frame of the trajectory the selected <br>> molecules will be reordered according to..." and so on. <br>> Does it mean that the ordering within each frame is <br>> INDEPENDENT on the prehistory and further moving of the <br>> group? In other words the first (the closest) molecules <br>> for different frames may be the different molecules?<br><br>Yes.<br><br>> <br>> For me, I would like to identify some molecules closest to <br>> the reference AT THE BEGINNING of my simulation and then <br>> to trace their evolution through the whole run. For this <br>> purpose the number of each molecule must be no changing <br>> from frame to frame! Can I do this with trjorder?<br><br>No, but it would not be difficult to modify the tools.<br>A probable easy solution would be to use trjorder only on the first<br>frame and write a pdb file as output. You can then look in the pbd file<br>for the residue numbers of the closest molecules and make an index file.<br><br>> <br>> And one more striking thing: even when I order each frame, <br>> the size of output (ordered) trr-file is about twice less <br>> than the size of input trr!<br><br>You probably have velocities in your trr, these are not written by trjorder.<br><br>Berk.<br><br><br>> <br>> With many thanks,<br>> Dmitri<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>