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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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