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Dear Sir,<br>
Thank you for your kind reply. If I want to fix the atom
positions still do I need to include angles, dihedrals in the topology
file? Waiting for your valuable kind reply.<br>
<br>
Rahul Karyappa<br>
<br><font face="Arial" size="2"><TABLE STYLE="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><b><i>-- Original Message --</i></b><br>From: Tsjerk Wassenaar <tsjerkw@gmail.com><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Date: Sat, 26 Nov 2005 12:42:39 +0100<br>Subject: Re: [gmx-users] How to fix the atom positions?<br><br>Hi Rahul,<br><br>It
depends how fixed you want. You could make it a freeze group and it
will stay exactly where and the way it is. However, a better idea is to
use position restraints, which will attach each atom to a reference
with a spring constant. For this you have to add a [
position_restraints ] section in the topology file. I think it's
chapter 5 of the manual.
<br><br>Cheers,<br><br>Tsjerk<br><br><DIV><SPAN CLASS="gmail_quote">On 11/26/05, <b class="gmail_sendername">Rahul Karyappa</b> <<A HREF="mailto:r.karyappa@ncl.res.in" TARGET="_blank">r.karyappa@ncl.res.in</A>> wrote:</SPAN><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear all,<br>
I want to fix the atom positions of one of my chain
structure. How can I do that? Do I need to make any changes in the
topology file or any other file? Please suggest me the way to do this.<br>
Thanking you in advance.<br>
<br>
Rahul Karyappa<br>
NCL, Pune<br>
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<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>
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