[gmx-users] Slow Runs

Dallas Warren Dallas.Warren at monash.edu
Fri Jan 28 00:12:19 CET 2011

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.warren at 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-bounces at gromacs.org
[mailto:gmx-users-bounces at 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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