vivek sharma wrote:
Hi there,
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.
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 ?
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.
I am not getting any idea of energy_excl option mentioned above, please
explain.
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.
-Justin
With Thanks,
Vivek
2008/10/12 Erik Lindahl <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Hi,
On Oct 10, 2008, at 12:46 PM, Justin A. Lemkul wrote:
I want to run MD over a part of my molecule , for few
residues only (not the whole molecule).
Can I do it using GROMACS ?
I searched for the online documentation and mailing list,
but unable to get appropriate information.
If somebody has already tried such things earlier, please
suggest and direct me for appropriate link and address.
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.
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.
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...
Cheers,
Erik
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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