[gmx-users] Running MD only for selected part of molecule
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 17 13:25:38 CEST 2008
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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
>
>
> 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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>>
>
>
>
> vivek sharma wrote:
>
>
>
> 2008/10/14 Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>
>
>
>
>
> 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 <lindahl at cbr.su.se
> <mailto:lindahl at cbr.su.se>
> <mailto:lindahl at cbr.su.se <mailto:lindahl at cbr.su.se>>
> <mailto:lindahl at cbr.su.se
> <mailto:lindahl at cbr.su.se> <mailto:lindahl at cbr.su.se
> <mailto:lindahl at cbr.su.se>>>
> <mailto:lindahl at cbr.su.se <mailto:lindahl at cbr.su.se>
> <mailto:lindahl at cbr.su.se <mailto:lindahl at cbr.su.se>>
>
> <mailto:lindahl at cbr.su.se
> <mailto:lindahl at cbr.su.se> <mailto:lindahl at cbr.su.se
> <mailto:lindahl at cbr.su.se>>>>>
>
>
>
> 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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