<div dir="ltr">Hi Justin,<br>Thanks for your reply...<br>and apologies for asking you again.<br><br>If I want to keep a part of my molecule fix, say part out of 12 angstrom radius from the ligand and also want to make avoid energy calculation for the same, (using energy_excl)<br>
Do I need to mention the separate group for that part of molecule, (as I already did to make that part position restrained), and next how I will mention those part in .mdp file...<br>Is it like...<br>energy_excl groupname protein/solvent (if I want to avoid energy calculation between the group and protein/solvent)<br>
or something else need to be done than that (like during genpr option).<br><br>Please explain....As I have no idea to play with such option...<br><br>My apologies again, if these small question irritates you.......<br><br>
With Thanks,<br>Vivek <br><br><div class="gmail_quote">2008/10/15 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d"><br>
<br>
vivek sharma wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Dear Justin,<br>
Thanks for your reply..<br>
But I am not getting how and where should I give the option of energy_excl. For freezing a part of molecule ?<br>
</blockquote>
<br></div>
In the .mdp file.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
what are the other checks to be done for the same ?<br>
<br>
</blockquote>
<br></div>
I don't know what you're asking.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
With Thanks,<br>
Vivek<div class="Ih2E3d"><br>
2008/10/14 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><br>
<br>
<br>
<br>
vivek sharma wrote:<br>
<br>
<br>
<br>
2008/10/14 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><div><div></div><div class="Wj3C7c"><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>><br>
<br>
<br>
<br>
<br>
vivek sharma wrote:<br>
<br>
Hi there,<br>
<br>
I tried the mdrun by keeping a group of residue position<br>
restrained, and it is working well (verified by comparing<br>
RMSD<br>
plot for the same), thanks for your suggestions regarding<br>
the same.<br>
But, I have seen that the part of the molecule I kept for<br>
PR is<br>
still having some motion, how can I keep that part rigid ?<br>
<br>
<br>
Position restraints do not necessarily guarantee that atomic<br>
positions stay absolutely fixed. Instead, there is an energy<br>
penalty for moving them, which could in some cases be overcome.<br>
<br>
<br>
I am not getting any idea of energy_excl option mentioned<br>
above,<br>
please explain.<br>
<br>
<br>
The freezegrps option can be used to fix atomic positions, but in<br>
this case large forces can be generated within the frozen<br>
group. As<br>
such, you can apply energygrp_excl to exclude energetic terms<br>
within<br>
the frozen group.<br>
<br>
<br>
Will it help me in reducing the time taken for the simulation if<br>
I'll keep the part of molecule frozen ?<br>
<br>
<br>
I've never used freezegrps for any large set of atoms, so maybe. If<br>
you've got surrounding solvent, though, the nonbonded interactions<br>
are still calculated between the frozen group and solvent, unless<br>
you turn that off too. But then it starts getting really<br>
unphysical, in my view.<br>
<br>
-Justin<br>
<br>
Thanks,<br>
~Vivek<br>
<br>
<br>
<br>
-Justin<br>
<br>
With Thanks,<br>
Vivek<br>
<br>
2008/10/12 Erik Lindahl <<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a><br>
<mailto:<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a>><br>
<mailto:<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a> <mailto:<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a>>><br>
<mailto:<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a> <mailto:<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a>><br>
<br></div></div>
<mailto:<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a> <mailto:<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a>>>>><div><div></div><div class="Wj3C7c">
<br>
<br>
<br>
Hi,<br>
<br>
<br>
On Oct 10, 2008, at 12:46 PM, Justin A. Lemkul wrote:<br>
<br>
<br>
I want to run MD over a part of my molecule ,<br>
for few<br>
residues only (not the whole molecule).<br>
Can I do it using GROMACS ?<br>
I searched for the online documentation and<br>
mailing list,<br>
but unable to get appropriate information.<br>
If somebody has already tried such things<br>
earlier, please<br>
suggest and direct me for appropriate link and<br>
address.<br>
<br>
<br>
Well, if your goal is to keep certain parts fixed<br>
and allow<br>
others to move, probably the easiest way to do it<br>
is to apply<br>
position restraints to the "fixed" part.<br>
<br>
<br>
You can also set parts of the system as a freeze<br>
group, in which<br>
case you can exclude all nonbonded interactions inside<br>
the freeze<br>
group with the energygrp_excl option in your mdp file.<br>
<br>
The main advantage of this is of course that you will<br>
improve<br>
performance if 99% of your system is frozen (although all<br>
interactions between the frozen and non-frozen parts still<br>
have to<br>
be calculated). On the other hand, completely freezing<br>
part<br>
of the<br>
system is not very realistic, and you're likely to get<br>
strange<br>
behavior in the interface...<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="Ih2E3d">
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
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<br>
========================================<br>
<br>
<br>
</div></blockquote><div><div></div><div class="Wj3C7c">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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<br>
========================================<br>
</div></div></blockquote></div><br></div>