[gmx-users] Rigid structure and flexible structure present in sing system

Justin A. Lemkul jalemkul at vt.edu
Thu May 12 14:49:41 CEST 2011

Luke Goodsell wrote:
> Thanks for the response, Justin.
>> Add a [constraints] directive for the molecule you want to make rigid and
>> use "constraints = none" in the .mdp file.  Thus, only the bonds manually
>> set to be constraints will be constrained.
> Great, this is a much better solution than the one I knew.
>> Note that by constraining one molecule but not another, you still can't save
>> any computing time, because the timestep of the simulation will still be
>> limited by any bonds that are still harmonic (especially X-H).  Your system
>> probably won't be stable with dt > 1 fs, even with some molecule(s)
>> constrained.
> I don't wish to increase dt (since I have another flexible molecule to
> consider). I wish only to not have gromacs calculate forces for every
> atom of my macromolecule in the system, as I am not interested in its
> dynamics and it is important primarily as a steric exclusion volume
> for the flexible molecule.

For this, constraints are irrelevant and you should investigate the freezegrps 
strategy Chris suggested.  Your original message said you wanted to preserve the 
relative coordinates, but freezing preserves absolute coordinates as well.

> Will applying a an all-bonds constraint on the macromolecule reduce
> the computation time?

Not at all.

>> I don't see any value in constraining one molecule but not another.  You
>> can't increase the timestep and you lose the ability to have rigid bonds.
>>  The argument can be made that a rigid bond is a better representation of
>> reality than a harmonic one for most biological applications, or any done at
>> ambient temperature, really.
> My flexible protein is folding in the presence of a rigid
> macromolecule that restricts region that the flexible protein can
> occupy. I will be investigating whether the flexibility of the
> macromolecule is important later, though previous work by
> collaborators suggests not. I therefore do not wish waste computer
> time calculating forces on the macromolecule.

If you freeze the larger molecule and apply energygrp_excl to it, then you may 
be able to speed up the calculations a little bit, but I don't think you'll gain 
a lot.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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