[gmx-users] gmx 3.1.4 vs 3.2.1

Berk Hess gmx3 at hotmail.com
Fri Nov 5 15:25:44 CET 2004

>From: Marcos Villarreal <arloa at mail.fcq.unc.edu.ar>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] gmx 3.1.4 vs 3.2.1
>Date: Fri, 5 Nov 2004 10:53:50 -0300
>I am testing gmx 3.1.4 vs 3.2.1. For several  systems, I have calculated  
>potential energy using the same pdb, topology, compiler, etc.
>When comparing the results,  the Long range part of the LJ energy is the 
>term that varies by a significant amount (about 10%) between the two
>versions. The LR-LJ energies calculated with 3.1.4 are always smaller than
>the calculated with 3.2.1.
>When you use a twin-range cutoff of 0.9-1.2 and compare with the results 
>with a single 1.2 nm cutoff, the sum of SR-LJ + LR-LJ of the twin-range 
>coincides with the result of the single cutoff when you use 3.2.1.
>Is this indicating that the LR-LJ term is not correctly calculated in gmx

I for your twin-range in 3.1.4 rcoulomb < rvdw?

The changes pages states for 3.1 to 3.2"

A bug has been fixed which could cause some LJ interactions at distances 
close to rvdw to be neglected when rvdw > rcoulomb (in practice this would 
only occur with GROMOS forcefields combined with PME).


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