[gmx-users] pressure_coupling

[tarak karmakar]

Dear All,

I want to keep the pressure at 1.0 bar during the NPT simulation. But
it is fluctuating around 130 bar. So can anyone please inform me
whether I have missed any keyword in my .mdp file OR is it because of
the tau_p which I set 1s 1.0 ps.
Thanks

The .mdp file is given below



; 7.3.3 Run Control
integrator              = md-vv                    ; md integrator
tinit                   = 0                     ; [ps] starting time for run
dt                      = 0.001                 ; [ps] time step for integration
nsteps                  = 15000000                ; maximum number of
steps to integrate, 0.001 * 15,00,000 = 15 ns
nstcomm                 = 1                     ; [steps] frequency of
mass motion removal
comm_grps               = Protein Non-Protein   ; group(s) for center
of mass motion removal

; 7.3.8 Output Control
nstxout                 = 10000        ; [steps] freq to write
coordinates to trajectory
nstvout                 = 10000        ; [steps] freq to write
velocities to trajectory
nstfout                 = 10000        ; [steps] freq to write forces
to trajectory
nstlog                  = 1000           ; [steps] freq to write
energies to log file
nstenergy               = 1000           ; [steps] freq to write
energies to energy file
nstxtcout               = 1000           ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision           = 1000          ; [real] precision to write
xtc trajectory
xtc_grps                = System        ; group(s) to write to xtc trajectory
energygrps              = System        ; group(s) to write to energy file

; 7.3.9 Neighbor Searching
nstlist                 = 1             ; [steps] freq to update neighbor list
ns_type                 = grid          ; method of updating neighbor list
pbc                     = xyz           ; periodic boundary conditions
in all directions
rlist                   = 1.2           ; [nm] cut-off distance for
the short-range neighbor list

nsttcouple              = 1
nstpcouple              = 1

; 7.3.10 Electrostatics
coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
rcoulomb                = 1.2           ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype                 = cut-off       ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw                    = 1.2           ; [nm] distance for LJ cut-off
DispCorr                = EnerPres      ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing          = 0.12          ; [nm] grid spacing for FFT
grid when using PME
pme_order               = 4             ; interpolation order for PME, 4 = cubic
ewald_rtol              = 1e-5          ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl                  = Nose-Hoover                   ; Nose-Hoover
temperature coupling
tc_grps                 = Protein    Non-Protein        ; groups to
couple seperately to temperature bath
tau_t                   = 1.0        1.0                ; [ps] time
constant for coupling
ref_t                   = 300        300                ; [K]
reference temperature for coupling

; 7.3.15 Pressure Coupling
pcoupl                  = MTTK                  ; pressure coupling
where box vectors are variable
pcoupltype              = isotropic             ; pressure coupling in
x-y-z directions
tau_p                   = 1.0                   ; [ps] time constant
for coupling
compressibility         = 4.5e-5                ; [bar^-1] compressibility
ref_p                   = 1.0                   ; [bar] reference
pressure for coupling

; 7.3.17 Velocity Generation
gen_vel                 = no            ; velocity generation turned off

; 7.3.18 Bonds
constraints             = h-bonds
constraint_algorithm    = SHAKE          ; SHAKE Constraint Solver
shake_tol               = 1.0e-5


-- 
Tarak