vivek sharma wrote:
2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
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.
Will it help me in reducing the time taken for the simulation if I'll
keep the part of molecule frozen ?
I've never used freezegrps for any large set of atoms, so maybe. If you've got
surrounding solvent, though, the nonbonded interactions are still calculated
between the frozen group and solvent, unless you turn that off too. But then it
starts getting really unphysical, in my view.
-Justin
Thanks,
~Vivek
-Justin
With Thanks,
Vivek
2008/10/12 Erik Lindahl <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> <mailto:[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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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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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