Hi,
is it possible to simulate rigid molecules with GROMACS?
It seems that the run option
constraints = all-angles
does this, but using it requires SHAKE, which cannot be used in energy
minimization.
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..
Also: what is the reference used for the constraints? Is it the force
field parameters, or the starting configuration..?
--
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Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
[email protected], p. 191 50632
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Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
[email protected]
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