Hi
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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