[gmx-users] Problem with pressure coupling

[Ondrej Marsalek]

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