[gmx-users] Differences in version 3.0 and 3.3

Cheong Wee Loong, Daniel dcheong at ihpc.a-star.edu.sg
Thu Aug 28 08:18:58 CEST 2008

Dear all,

I was running an NPT molecular dynamics simulation on a system of 6 protein strands.  I am using Gromacs version 3.3 and for some specific purposes, I was only using version 3.0.  Starting from the same input structure, forcefield (OPLS) and same run parameters, I noticed that the Coul 1-4 interactions are different in the two versions, even in the very first step in calculating the energy of the starting configuration.  All the other interactions are the same except for the Coul 1-4.  The charges are obviously the same, and the same fudgeQQ value was used.  Is there an inherent difference in how the two versions calculate the Coul 1-4 interactions?

The second difference I noticed involves the pressure coupling.  I was doing a semiisotropic Berendsen pressure coupling.  In version 3.3, the pressure scaling seems to work properly, as in, the pressure in the xy direction and in the z direction averages out to the pressure value I had set.  However in version 3.0, the scaling seems to work properly in the xy direction, but the pressure in the z direction does not go to the desired pressure.  I am using in both cases, a time constant of 0.5ps, a pressure of 1 bar, and a compressibility of 4.5e-5 for both the xy and z directions.  I am interested in the surface tension, so if the normal pressure is off, then so is the surface tension.  Again is this difference in behavior known or expected? Or am I missing something simple and fundamental here?

Any advice or suggestions will be greatly appreciated.

Thank you.


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