[gmx-users] Re: Problem with pressure coupling

[Ondrej Marsalek]

Hi again,

I have made available a testcase that reproduces the problem here:

http://marge.uochb.cas.cz/~marsalek/tmp/test-volume-drift.tar.bz2

To see the problem, use grompp
from GMX 4.5.1 and run the resulting tpr. Then extract the volume:

echo Volume | g_energy -f ener.edr -o volume

and observe the drift. I would be very grateful if someone could help
me confirm the behavior.

I have found one more thing indicative of this being a bug in 4.5.1.
If I use grompp from 4.0.7 and then run the tpr using 4.5.1 it runs
fine, just as it runs in 4.0.7. The tpr produced by grompp from 4.5.1
has the drift in box volume when run in 4.5.1. Of course, it will not
run in 4.0.7, so there is no way of testing that.

Thanks for any help on this,
Ondrej


On Thu, Sep 23, 2010 at 15:16, Ondrej Marsalek
<ondrej.marsalek at gmail.com> wrote:
> Dear all,
>
> running a box of neat water with the below mdp file in GROMACS 4.5.1
> results in a fast linear increase of the volume of the box, the water
> getting torn into clusters. The same simulation in 4.0.7 (with
> nstcalcenergy removed, of course) runs just fine, with the box volume
> stable and fluctuating. In 4.5.1 the problem can be fixed by setting
> nstlist = 1. I assume this would also be the case for other positive
> numbers. The same behavior can be seen for the Parrinello-Rahman
> barostat. I can of course provide full testcases ready to run, if
> needed.
>
> This looks like a bug to me. Can anyone help me resolve this?
>
> Thanks,
> Ondrej
>
>
> ; RUN CONTROL PARAMETERS
> integrator               = md
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 5000
> comm-mode                = Linear
> nstcomm                  = 10
>
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 100
> nstcalcenergy            = 10
> nstenergy                = 100
> nstxtcout                = 100
> xtc-precision            = 1000
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist                  = -1
> ns_type                  = grid
> pbc                      = xyz
> periodic_molecules       = no
> rlist                    = 1.3
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype              = PME-Switch
> rcoulomb-switch          = 0.6
> rcoulomb                 = 0.8
> vdw-type                 = Shift
> rvdw-switch              = 0.6
> rvdw                     = 0.8
> DispCorr                 = EnerPres
> fourierspacing           = 0.12
> pme_order                = 4
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> optimize_fft             = yes
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> Tcoupl                   = v-rescale
> tc-grps                  = system
> tau_t                    = 0.5
> ref_t                    = 300
> Pcoupl                   = berendsen
> Pcoupltype               = isotropic
> tau_p                    = 1
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel                  = no
>
> ; OPTIONS FOR BONDS
> constraints              = none
>