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

Luke Goodsell luke.goodsell at gmail.com
Thu May 12 11:24:29 CEST 2011

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.

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

> 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.

> -Justin


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