[gmx-users] problems with pressure control when using implicit solvent

[Ming Tang]

Dear all,

I am doing a modelling which consist of a peptide of 40 residues. I am using Implicit solvent and controlled the pressure. However, the box keeps shrinking until the system collapse if I use PBC.

If I remove PBC, the pressure will always be 0. I guess this is due to the together use of implicit solvent, pressure control and non-PBC condition.  Can anyone give me some advices?

Thanks,
Tony

title                        = charmm27
define                   = -DPOSRES        ; position restrain the protein
; Run parameters
integrator            = md-vv                               ; leap-frog integrator
nsteps                  = 5000000            ; 2 * 5000000 = 10 ns
dt                            = 0.002                  ; 2 fs
; Output control
nstxout                                = 100000              ; save coordinates
nstvout                                = 100000              ; save velocities
nstxtcout             = 1000
nstenergy           = 1000                   ; save energies
nstlog                    = 1000                   ; update log file

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; nblist cut-off
cutoff-scheme                  = group
rlist                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = cut-off
rcoulomb-switch          = 0.8
rcoulomb                 = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 2
epsilon_rf               = 0
; Method for doing Van der Waals
vdw-type                 = cut-off
; cut-off lengths
rvdw-switch              = 0.8
rvdw                     = 1.2

; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing                = single
; Number of time points to use for specifying annealing in each group
annealing-npoints        = 4
; List of times at the annealing points for each group
annealing-time           = 0 10 20 30
; Temp. at each annealing point, for each group.
annealing-temp           = 10 100 200 300

; Temperature coupling is on
tcoupl                   = nose-hoover  ; nose-hoover thermostat
tc-grps                  = System             ; coupling groups - more accurate
tau_t                     = 5                          ; time constant, in ps
ref_t                      = 300                     ; reference temperature, one for each group, in K

pcoupl                  = MTTK                 ; Pressure coupling on in NPT
pcoupltype         = isotropic           ; uniform scaling of box vectors
tau_p                    = 5                          ; time constant, in ps
ref_p                     = 1.0                      ; reference pressure, in bar
compressibility = 4.5e-5                ; isothermal compressibility of water, bar^-1
refcoord_scaling = com


; Periodic boundary conditions
pbc                         = xyz                      ; 3-D PBC

; Dispersion correction
DispCorr               = EnerPres          ; account for cut-off vdW scheme

; Velocity generation
gen_vel                                = no                       ; Velocity generation is off

; IMPLICIT SOLVENT ALGORITHM
implicit-solvent         = GBSA

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb-algorithm             = OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 1.2
; Dielectric coefficient of the implicit solvent
gb-epsilon-solvent       = 80
; Salt concentration in M for Generalized Born models
gb-saltconc              = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb-obc-alpha             = 1
gb-obc-beta              = 0.8
gb-obc-gamma             = 4.85
gb-dielectric-offset     = 0.009
sa-algorithm             = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa-surface-tension       = -1