[gmx-users] Minimal box vectors chosen by the pressure integration

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Tue Nov 25 19:36:51 CET 2014

On 25.11.2014 17:13, Mirco Wahab wrote:
> I'm somehow able to drive a 1000-water (mixed phase-)system,
> starting from a ~50nm^3 box into a gas phase (0.001 bar,
> resulting in a 230nm^3 box. This does work so far. When
> increasing the applied pressure (Parrinello-Rahman) into
> the liquid zone (eg. 0.2 bar), the system shrinks eventually
> until a box size of 7.39492nm is reached. Then, the shrinking
> stops, the box contains a water drop + vacuum.
> How does gromacs determine the minimal box size
> that it  allows the pressure algorithm to induce?
> Is this based on the (in this case) PME grid or
> on the domain decomposition?

After inspecting the log-file, I have the suspicion it
depends on th PME grid. The large box w/dilute vapor
started with a PME grid after optimization:

  step  650: the PME grid restriction limits the PME load balancing to a 
coulomb cut-off of 7.311
  step 1050: timed with pme grid 6 6 6, coulomb cutoff 7.311: 32.4 M-cycles
                optimal pme grid 6 6 6, coulomb cutoff 7.311

If I take a snapshot of this system (p=0.2bar, stuck at a=7.39nm)
and *start it again* allowing gromacs to optimize a new PME grid,
the system ends up after very short time in it's correct (liquid)
phase (box size a = ~ 3.7 nm).

Maybe running into a volume-change restriction would reward a warning
in the log-file?

Thanks & regards


More information about the gromacs.org_gmx-users mailing list