<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="MS Exchange Server version 6.5.7651.59">
<TITLE>problems about trjconv</TITLE>
</HEAD>
<BODY>
<!-- Converted from text/plain format -->
<P><FONT SIZE=2>Hi, All<BR>
<BR>
I do my md simulation for 30ns, but after 20ns the protein move out of the box, so it seems that the protein is broken in .trr file. I try to use trjconv to put the protein back into the box and make the protein whole. The command is like below:<BR>
trjconv trjc -f *.trr -o out.trr -s *.tpr -pbc nojump -center rect<BR>
<BR>
But after run the trjcov command, some parts of the protein is till out of box, and seems like broken.<BR>
Is there anyone meed the same problem can tell me how to resolve this problem.<BR>
<BR>
Thank you very much<BR>
<BR>
Di,Pan<BR>
<BR>
Di,Pan<BR>
<BR>
<BR>
</FONT>
</P>
</BODY>
</HTML>