Luke Goodsell wrote:
Hi,
For a while I've been looking for a way to include a rigid
(macromolecular) structure and a flexible (small-protein) structure in
a single system and have not had much success.
I looked for a way to apply a different set of constraints to each
structure, but couldn't find one. I looked into modifying the topology
file, but the only method I could find was to artificially increase
the mass of every atom in the rigid structure and this does not save
any computing time.
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.
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.
Does anyone know how I can fix the relative co-ordinates of one
structure and only calculate the MD of another?
Any constructive criticism (even if to inform me that I'm doing
something ridiculous) is very gratefully received.
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.
-Justin
Kind regards,
Luke
--
========================================
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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