<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=UTF-8" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
What I meant is: do you save the trajectory every 0.1ps? <br>
<br>
The problem seem to be that trjconv isn't able to find any frame
between t=0.1ps and t=0.2ps. So, if you save you data every 1ps,
there's no data in your .xtc file. This is why Xavier suggested to use
gmxcheck, that will tell you both how many steps you have in the xtc
and what's the timestep.<br>
<br>
I agree that trjconv is more convenient than VMD for this.<br>
Ran.<br>
<br>
OZGE ENGIN wrote:
<blockquote cite="mid1195492371.500cb35cOZENGIN@KU.EDU.TR" type="cite">
<pre wrap="">Of course, I am performing a 40 ns simulation, and 14 ns of it has been finished.
What may be the problem? I know, I can extract specific frames via VMD, but it changes atom types after saving in pdb format.
-----Original Message-----
From: Ran Friedman <a class="moz-txt-link-rfc2396E" href="mailto:r.friedman@bioc.uzh.ch"><r.friedman@bioc.uzh.ch></a>
To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Date: Mon, 19 Nov 2007 17:53:16 +0100
Subject: Re: [gmx-users] trjconv does not work
I see. Do you have any structure between t=0.1ps and t=0.2ps?
Ran.
OZGE ENGIN wrote:
</pre>
<blockquote type="cite">
<pre wrap="">The command line ws the following:
trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb
</pre>
</blockquote>
<pre wrap=""><!---->
_______________________________________________
gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please search the archive at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
Can't post? Read <a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a>
_______________________________________________
gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please search the archive at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
Can't post? Read <a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a>
</pre>
</blockquote>
<br>
</body>
</html>