[gmx-users] Re: Problem with pressure coupling

[Ondrej Marsalek]

And I have just noticed that this was an mdp after some testing with
changed values. It behaves the same also with the more sensible values
below. Moreover, it looks like something that will not be sensitive to
the details of the the FF evaluation.

rlist                    = 1.2
rcoulomb-switch          = 0.8
rcoulomb                 = 1
rvdw-switch              = 0.8
rvdw                     = 1


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
>