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On 14/07/2011 11:28 AM, Itamar Kass wrote:
<blockquote cite="mid:4E1E4639.80705@monash.edu" type="cite">
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Hi,<br>
<br>
I wish to force my system to maintained an Hbond during a
simulation. In order to do so I am using a distance restraint
protocol, with the following parameters:<br>
<br>
In the topology file<i>:<br>
<br>
</i><tt>[ distance_restraints ]<br>
; ai aj type index type' low up1 up2 fac<br>
2786 3262 1 0 2 0.295 0.305 0.315 1.0 ;</tt><tt> </tt><br>
<br>
and in the run input file:<br>
<br>
<tt>; DISTANCE RESTRAINTS<br>
disre = simple<br>
disre_weighting = equal<br>
disre_fc = 20<br>
disre_mixed = yes<br>
disre_tau = 10<br>
nstdisreout = 1000</tt><br>
<br>
The atoms numbering was taken from the topology file ( <i>268LYSH
NZ 2786 3.939 7.037 5.060 0.2307 -0.0416 -0.3125</i> and
<i>320GLU OE1 3262 3.872 6.806 4.875 -0.2077 -0.0055
-0.1229</i> ) and is based the crystal structure (for atoms and
distance).</blockquote>
<br>
Those lines are from .gro files, not topology files.
[distance_restraints] are specific to a [moleculetype], and must use
the atom indices established in the [atoms] section of the
[moleculetype]. Anything found in a .gro file is irrelevant, but
might be fortuitously accurate.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:4E1E4639.80705@monash.edu" type="cite"> When I
looked into the tpr file, the same atoms are numbered differently.<br>
<br>
My questions are:<br>
1. should I use the numbering as given in the topology file?<br>
2. Am I using it correctly? Should I use a force bigger then 20kJ?<br>
<br>
All the best,<br>
Itamar<br>
<br>
PS I am using GROMACS VERSION 4.0.7 in double precisin on a Linux
cluster.<br>
<pre class="moz-signature" cols="72">--
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a>
============================================</pre>
</blockquote>
<br>
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