[gmx-users] Equilibrating systems of rigid molecules

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 9 20:33:21 CET 2009

Jussi Lehtola wrote:
> 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..?
Unfortunately this is not possible. With constraints = all-angles you 
still have flexible dihedrals. You can also use all-angles with LINCS if 
you increase the iteration count (lincs-iter).

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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