vivek sharma wrote:
Dear Justin,
Thanks for your reply..
But I am not getting how and where should I give the option of
energy_excl. For freezing a part of molecule ?
In the .mdp file.
what are the other checks to be done for the same ?
I don't know what you're asking.
-Justin
With Thanks,
Vivek
2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
vivek sharma wrote:
2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> <mailto:[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]>>
<mailto:[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> <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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
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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