[gmx-users] pathologically expanding box

[Greg Bowman]

Hello,

Has anyone else experienced a pathologically expanding box during 
equilibration in the NPT ensemble?  I've solvated my system with 
editconf/genbox, energy minimized, equilibrated in NVT with the protein 
coordinates restrained, and then equilibrated in NPT without any 
position restraints.  During the NPT equilibration all the box 
dimensions are doubling and the density decreases drastically.

I'm using the v-rescale thermostat and the Berendsen barostat in gromacs 
4.5.3 with the AMBER03 force field and tip3p water.  I've also tried 
OPLSAA with SPC water, a number of different box types (cubic, 
octahedral, dodecahedral), and shorter tau_t and tau_p settings.  I also 
tried adding another energy minimzation step between my NVT and NPT phases.

My mdp settings for the NPT ensemble are below.

Thanks for your help.

Greg

; RUN CONTROL PARAMETERS
;define              = -DPOSRES
integrator          = md
tinit               = 0
nsteps              = 50000
dt                  = 0.002000
comm-mode           = linear
nstcomm             = 4

; CONSTRAINTS
constraints         = all-bonds
lincs_order         = 6
lincs_iter          = 2

; NEIGHBORSEARCHING PARAMETERS
ns_type             = grid
nstlist             = 4
rlist               = 1.2
pbc                 = xyz

; ELECTROSTATICS
coulombtype         = pme ;-switch
rcoulomb            = 1.2
;rcoulomb-switch     = 0.800000
fourierspacing      = 0.120000
fourier_nx          = 0
fourier_ny          = 0
fourier_nz          = 0
pme_order           = 6
ewald_rtol          = 0.000001
ewald_geometry      = 3d
epsilon_surface     = 0
optimize_fft        = yes
epsilon_r           = 80

; VDW
vdw-type            = switch
rvdw                = 1.2
rvdw-switch         = 1.1
DispCorr            = EnerPres

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout             = 0
nstvout             = 0
nstfout             = 0
nstlog              = 0
energygrps          = System
nstenergy           = 100
nstcalcenergy       = 1
nstxtcout           = 0
xtc-grps            = Protein

Tcoupl              = v-rescale
tau_t               = 0.5
tc-grps             = System
ref_t               = 300
ld_seed             = -1

Pcoupl              = berendsen
Pcoupltype          = isotropic
tau_p               = 5
compressibility     = 4.5e-5
ref_p               = 1.0

gen_vel             = yes
gen_temp            = 300.0
gen_seed            = -1