Rgardng the Coul 1-4 interactions, are you only changing the
executable in this comparison,
or are you also (perhaps unintentionally) changing the .itp files? If
so, could the
difference be related to changes to the forcefield files as mentioned here:
http://www.gromacs.org/pipermail/gmx-users/2006-April/021184.html
Chris.
-- original message --
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.
Daniel
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