<div dir="ltr"><br><br><div class="gmail_quote">2008/10/14 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;">
Hi there,<br>
<br>
I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same.<br>
But, I have seen that the part of the molecule I kept for PR is still having some motion, how can I keep that part rigid ?<br>
</blockquote>
<br></div>
Position restraints do not necessarily guarantee that atomic positions stay absolutely fixed. Instead, there is an energy penalty for moving them, which could in some cases be overcome.<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;">
I am not getting any idea of energy_excl option mentioned above, please explain.<br>
<br>
</blockquote>
<br></div>
The freezegrps option can be used to fix atomic positions, but in this case large forces can be generated within the frozen group. As such, you can apply energygrp_excl to exclude energetic terms within the frozen group.</blockquote>
<div><br>Will it help me in reducing the time taken for the simulation if I'll keep the part of molecule frozen ?<br><br>Thanks,<br>~Vivek <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<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<br>
<br>
2008/10/12 Erik Lindahl <<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 class="Ih2E3d"><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 , for few<br>
residues only (not the whole molecule).<br>
Can I do it using GROMACS ?<br>
I searched for the online documentation and mailing list,<br>
but unable to get appropriate information.<br>
If somebody has already tried such things earlier, please<br>
suggest and direct me for appropriate link and address.<br>
<br>
<br>
Well, if your goal is to keep certain parts fixed and allow<br>
others to move, probably the easiest way to do it is to apply<br>
position restraints to the "fixed" part.<br>
<br>
<br>
You can also set parts of the system as a freeze group, in which<br>
case you can exclude all nonbonded interactions inside 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 improve<br>
performance if 99% of your system is frozen (although all<br>
interactions between the frozen and non-frozen parts still have to<br>
be calculated). On the other hand, completely freezing part of the<br>
system is not very realistic, and you're likely to get strange<br>
behavior in the interface...<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
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-- <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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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