vivek sharma wrote:
Hi Justin,
Thanks for your reply...
and apologies for asking you again.
If I want to keep a part of my molecule fix, say part out of 12 angstrom
radius from the ligand and also want to make avoid energy calculation
for the same, (using energy_excl)
Do I need to mention the separate group for that part of molecule, (as I
already did to make that part position restrained), and next how I will
mention those part in .mdp file...
Is it like...
energy_excl groupname protein/solvent (if I want to avoid
energy calculation between the group and protein/solvent)
or something else need to be done than that (like during genpr option).
Pretty much. See the manual, section 7.3.18 for an example.
-Justin
Please explain....As I have no idea to play with such option...
My apologies again, if these small question irritates you.......
With Thanks,
Vivek
2008/10/15 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
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]> <mailto:[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]>>
<mailto:[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]>>>
<mailto:[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>
<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> <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 <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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