[gmx-users] Pressure Coupling Problem

[Joe Joe]

Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
run NVE it conserves energy with appropriate parameter settings. If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the system just continuously expands. My parameters are as follows.
Any ideas?

Best,

Ilya

;
;       File 'mdout.mdp' was generated
;       By user: relly (508)
;       On host: master.simprota.com
;       At date: Fri Mar  6 20:17:33 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include                  =
; e.g.: -DI_Want_Cookies -DMe_Too
define                   =

; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.004
;nsteps                   = 250000
nsteps                   = 2500000
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part          = 1
init_step                = 0
; mode for center of mass motion removal
comm_mode                = linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm_grps                = system

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0

; Output frequency for energies to log file and energy file
nstlog                   = 10
nstenergy                = 10
; Output frequency and precision for xtc file
nstxtcout                = 250
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps                 = protein
; Selection of energy groups
energygrps               =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 5
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic_molecules       = no
; nblist cut-off
rlist                    = 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = PME
rcoulomb-switch          = .9
rcoulomb                 = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r                = 80
epsilon_rf               = 1
; Method for doing Van der Waals
vdw-type                 = Switch
; cut-off lengths
rvdw-switch              = .9
rvdw                     = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Seperate tables between energy group pairs
energygrp_table          =
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1.e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = V-rescale
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1
ref_t                    = 298.0
; Pressure coupling
Pcoupl                   = Berendsen
Pcoupltype               = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 10
compressibility          = 4.5e-5
ref_p                    = 1.01325
; Scaling of reference coordinates, No, All or COM
refcoord_scaling         = No
; Random seed for Andersen thermostat
andersen_seed            = 815131
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