[gmx-users] Re: Different system volumes from gromacs versions 3.2.1 and 3.3.1

[Perttu Niemela]

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.

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.

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 (?)

Regards,
Perttu Niemela