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On 7/07/2011 3:29 AM, Mr Bernard Ramos wrote:
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cite="mid:1309973390.96133.YahooMailClassic@web161503.mail.bf1.yahoo.com"
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<div>Hi Mark and everyone!</div>
<div> </div>
<div>This has been a previous topic though and thanks Mark
for the reply.</div>
<div>What I need to do is to calculate the potential
energy (energy minimzation) of a molecule at every fixed
pairs of dihedrals (phi, psi).</div>
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<br>
So you really have a problem about creating particular conformations
of peptides, and then doing some EM on them. Your original email
didn't say that, so I wasn't able to give relevant help.<br>
<br>
EM is only good for local optimization, so just applying a large
force constant will not necessarily find a sensible minimum that
satisfies the restraint. A stinking mess is a fairly likely result.
MD has a better chance of getting to the region of a minimum you
seek, but will still be fiddly.<br>
<br>
A good molecule building program will allow you to rotate the parts
of the molecule about a dihedral to set the value you want. *Then*
do EM. If you hadn't pre-supposed the form of the solution to your
underlying problem, you'd have got what I think is more effective
help last time :-)<br>
<br>
If you have a lot of conformers to generate, then Google around to
see if there are any useful tools available.<br>
<br>
Mark<br>
<br>
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<div> I did the suggestions on <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints"><u><font
color="#0000ff">http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints</font></u></a>.
In fact what follows is the entry I placed in my
topol.top </div>
<div> </div>
<div>[ dihedral_restraints ]</div>
<span lang="">
<div>; ai aj ak al type label phi dphi kfac power</div>
</span>
<div>5 1 40 38 1 1 30 0 1 2 </div>
<div>12 40 38 34 1 1 10 0 1 2 </div>
<div> </div>
<div>I also added the following in my mdp file </div>
<div>dihre = yes</div>
<div>dihre_fc = 10000</div>
<div> </div>
<div>I removed disre_tau and nstdihreout as they are no
longer needed in the recent gromacs versions.
Unfortunately, after checking the dihedral angles, they
appear to be far from the set value of (phi=30, psi=10).
I understand that we are restraining the angles and not
constraining/fixing them. Is there a way we can have the
resulting phi and psi as close to the required values? I
get values 15 degrees away from the original settings.
Your help is greatly appreciated. </div>
<div>One more question. This restraining will not affect
the final potential energy right?</div>
<div>Bernard</div>
<br>
--- On <b>Mon, 6/27/11, Mark Abraham <i><a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a></i></b>
wrote:<br>
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255); padding-left: 5px; margin-left: 5px;"><br>
From: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
Subject: Re: [gmx-users] placing dihedral constraints<br>
To: "Discussion list for GROMACS users"
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
Date: Monday, June 27, 2011, 5:38 PM<br>
<br>
<div id="yiv350602181">On 06/27/2011 07:31 PM, Mr
Bernard Ramos wrote:
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<td valign="top">Hi!
<div><br>
</div>
<div>I would like to freeze two
dihedrals/torsion angles but allow the
rest (i.e. bonds, angles) to relax during
energy minimization and MD. How do I go
over applying constraints? Thanks.</div>
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<br>
See <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints"
rel="nofollow" target="_blank">http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints</a>
to sort out some nomenclature. You probably want a
dihedral restraint with a strong force constant
(though other approaches are possible). See relevant
parts of chapters 4 and 5. Work by analogy from the
[dihedrals] and [position_restraints] sections in your
existing [moleculetype].<br>
<br>
Mark<br>
</div>
<br>
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