You will need to provide more details on the system. How many atoms, what sort of computer system is it being run on, how many nodes, copy of the mdp file etc.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Denny Frost Sent: Friday, 28 January 2011 9:34 AM To: Discussion list for GROMACS users Subject: [gmx-users] Slow Runs 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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