[gmx-users] Slow Runs

Denny Frost dsfrost at cableone.net
Thu Jan 27 23:34:17 CET 2011

I am taking over a project for a graduate student who did MD using Gromacs
3.3.3.  I now run similar simulations with Gromacs 4.5.1 and find that they
run only about 1/2 to 1/3 as fast as the previous runs done in Gromacs
3.3.3.  The runs have about the same number of atoms and both use opls force
fields.  The mdp files is virtually the same (I copied them).  The only
major difference is that my runs have difference species and thus have
different (although smaller) itp files.  The runs are stable and give
reasonable thermodynamic properties - they're just slow.  Has anyone had any
experience with something like this?
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