[gmx-users] Equilibrating systems of rigid molecules

Dimitris Dellis ntelll at gmail.com
Sat Jan 10 14:47:32 CET 2009


Jussi Lehtola wrote:
> Hi,
> is it possible to simulate rigid molecules with GROMACS?
Yes, rigid up to shake accuracy, but only using constraints in topol.
> It seems that the run option
> 	constraints = all-angles
> does this, but using it requires SHAKE, which cannot be used in energy
> minimization.
This, except dihedrals that are not constrained by constraints=all-angles,
could lead to wrong results in case it seems to work - degrees of 
freedom issue.
> How can one generate suitable starting configurations of rigid
> molecules? At least using a configuration minimized without any
> constraints seems to crash in the first step since SHAKE cannot satisfy
> the constraints in the allowed number of steps..
Write your own utility that creates a box of rigid molecules or
use a configuration from another program that handles rigid molecules 
(after converting format)
> Also: what is the reference used for the constraints? Is it the force
> field parameters, or the starting configuration..?

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