[gmx-users] funny zero-step mdrun results in 4.0.3

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 11 07:48:57 CET 2009

David Mobley wrote:
> All,
> I'm trying to run a zero-step mdrun in 4.0.3 (basically just to
> evaluate the energy of a specific configuration). I've done this test
> in 3.3.x and am trying to check if 4.0.3 gives the same energies. I'm
> also comparing against another simulation package. To this end, I have
> my starting coordinates (in a gro file) in higher precision than
> normal.
> Anyway, this all works fine in 3.3.x, but in 4.0.3 the "end"
> coordinates after zero steps are clearly very very wrong (as are the
> resulting energies -- I have three molecules in my system and, for
> example, I'm getting a bond energy of hundreds of thousands of kJ/mol
> in 4.0.3, but not in 3.3.x.
> Clearly I must be doing something wrong. Has there been a change in
> acceptable gro formats in 4.0.x?
> I'm attaching an mdp file, and the starting gro file (acetamide.gro)
> as well as the output gro file (fullcoupling.gro).
> Thanks,
> David

Both your gro files are wrong, the definition of gro files has never 
changed. Do you mean to say this has ever worked?

If you want high precision use g96.

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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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