[gmx-users] Equilibrating systems of rigid molecules

Jussi Lehtola jussi.lehtola at helsinki.fi
Fri Jan 9 17:30:41 CET 2009


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

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..?
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50632
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi

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