Hi again,
I used the "Martini" version of the force-field. The difference in volume
is only about 1 percent, but still much larger than the fluctuations which
are about 0.1 percent. The effect is very systematic though, and it can be
disturbing if you have carelessly run simulations with different versions
and try to compare the results :)
The reason why I am testing this is that we observed a similar effect with
other force fields too, and could not explain it. For example, area per
lipid values for lipid bilayers (all-atom) displayed a similar dependency
on gromacs version, but now with 5 to 10 percent differences. I am not yet
sure if this is caused by the same effect at all, but continuing to test
on it.
If anybody has seen similar effects and/or has other possible
explanations, would be nice to hear them.
Regards,
Perttu
On Tue, 8 Jan 2008 15:39:51 +0200 (EET)
Perttu Niemela <[EMAIL PROTECTED]> wrote:
Hi All,
In December here was a short discussion about a water system, for which
gromacs versions 3.2.1 and 3.3.1 produced different average volumes. I have
experienced similar thing with Marrink's coarse grained water (about 1500
beads in the box), but to opposite direction.
Just by curiosity: which version the ff you use?
My test runs with gromacs 3.1.4 and 3.2.1 always give a larger average
volume than versions 3.3.1. and 3.3.2. The difference is much larger than the
fluctuations. I use berendsen barostat (isotropic; p = 1 atm) and thermostat
(T=300K). In my simulations, the off-diagonal terms of the virial are very
close to zero. Additionally, I have tested using simple cutoffs instead of
switch/shift functions, but it does not affect the general conclusion.
How much is the difference you observe and which percentage of the volume
does this represent?
Can it be that the difference in calculating the kinetic energy (and
temperature) leads to the observed volume difference? I did a quick test to
modify the code of gromacs v. 3.3.1 such that it calculates kinetic energy
exactly like in v. 3.2.1, and the volume jumps back up.
Can somebody please confirm, if this is expected? I cannot fully understand
how a more exact calculation of the kinetic energy would lead to a
significant change of the average volume (?)
Well a change in temperature should affect the volume of course, so the
change in estimation of the kinetic energy will affect the volume but
the effect should be very small!
XAvier
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