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.
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