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

Justin A. Lemkul jalemkul at vt.edu
Wed May 11 18:47:26 CEST 2011

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.


> Kind regards,
> Luke


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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