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

[David Mobley]

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
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