<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style id="owaParaStyle" type="text/css">P {margin-top:0;margin-bottom:0;}</style>
</head>
<body ocsi="0" fpstyle="1" bgcolor="#ffffff">
<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 13px;">
<div style="">editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_box.gro -center x/2 y/2 z/2 -box x y z<br>
genbox -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o they_are_in_the_same_box_now.gro -p topol.top<br>
<br>
hth,<br>
<br>
lina<br>
</div>
<div style="font-family: Times New Roman; color: rgb(0, 0, 0); font-size: 16px;">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF122947"><font color="#000000" face="Tahoma" size="2"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of Mark Abraham [Mark.Abraham@anu.edu.au]<br>
<b>Sent:</b> Thursday, November 04, 2010 5:53 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] center peptide in simulation box<br>
</font><br>
</div>
<div></div>
<div>On 3/11/2010 9:04 PM, leila karami wrote:
<blockquote type="cite"><span style="font-family: arial,helvetica,sans-serif;">Dear Mark Abraham</span><br style="font-family: arial,helvetica,sans-serif;">
<br style="font-family: arial,helvetica,sans-serif;">
<span style="font-family: arial,helvetica,sans-serif;">In March 2010, In reply to question about [center peptide in simulation box], You answered:</span><br style="font-family: arial,helvetica,sans-serif;">
<pre style="font-family: arial,helvetica,sans-serif;">OK, well keep playing with the trjconv options and choosing sensible groups for centering until you find something that pleases you. You may
need to do two different trjconv operations - one to center the peptide and one to group the waters in the same periodic cell as the peptide.
I want to know how can I do last (group the waters in the same periodic cell as the peptide)?
</pre>
</blockquote>
<br>
I'd find the answer to this by reading trjconv -h and experimenting :-)<br>
<br>
Mark<br>
</div>
</div>
</div>
</body>
</html>