<div dir="ltr">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>I am not getting any idea of energy_excl option mentioned above, please explain.<br><br>With Thanks,<br>
Vivek<br><br><div class="gmail_quote">2008/10/12 Erik Lindahl <span dir="ltr"><<a href="mailto:lindahl@cbr.su.se">lindahl@cbr.su.se</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;">
Hi,<div class="Ih2E3d"><br>
<br>
On Oct 10, 2008, at 12:46 PM, Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
I want to run MD over a part of my molecule , for few residues only (not the whole molecule).<br>
Can I do it using GROMACS ?<br>
I searched for the online documentation and mailing list, but unable to get appropriate information.<br>
If somebody has already tried such things earlier, please suggest and direct me for appropriate link and address.<br>
</blockquote>
<br>
Well, if your goal is to keep certain parts fixed and allow others to move, probably the easiest way to do it is to apply position restraints to the "fixed" part.<br>
</blockquote>
<br></div>
You can also set parts of the system as a freeze group, in which case you can exclude all nonbonded interactions inside the freeze group with the energygrp_excl option in your mdp file.<br>
<br>
The main advantage of this is of course that you will improve performance if 99% of your system is frozen (although all interactions between the frozen and non-frozen parts still have to be calculated). On the other hand, completely freezing part of the system is not very realistic, and you're likely to get strange behavior in the interface...<br>
<br>
Cheers,<br>
<br>
Erik<div class="Ih2E3d"><br>
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