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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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