[gmx-users] NVT and NPT equilibration

[Pandya, Akash]

Hi all,

I want to equilibrate my system and NVT worked fine for me converging onto the 300K set point. However, with the NPT part my average pressure is very low (0.22 bar) compared to the 1 bar set point. Is it necessary to do both equilibration steps in order to progress through to the production MD run? Or will NVT be suffice. I have copied my NPT mdp file to this email.

define                 = -DPOSRES        ; position restrain the protein
; Run parameters
integrator           = md                    ; leap-frog integrator
nsteps                 = 25000                             ; 2 * 25000 = 50 ps
dt                             = 0.002                          ; 2 fs
; Output control
nstxout               = 100                   ; save coordinates every 0.2 ps
nstvout               = 100                   ; save velocities every 0.2 ps
nstenergy           = 100                   ; save energies every  0.2 ps
nstlog                  = 100                   ; update log file every 0.2 ps
; Bond parameters
continuation      = yes                    ; Restarting after NVT
constraint_algorithm = lincs        ; holonomic constraints
constraints         = all-bonds         ; all bonds (even heavy atom-H bonds) constrained
lincs_iter            = 1                       ; accuracy of LINCS
lincs_order        = 4                       ; also related to accuracy
; Neighborsearching
ns_type              = grid                   ; search neighboring grid cells
nstlist                  = 5                       ; 10 fs
rlist                      = 1.0                    ; short-range neighborlist cutoff (in nm)
rcoulomb           = 1.0                    ; short-range electrostatic cutoff (in nm)
rvdw                    = 1.0                    ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME                 ; Particle Mesh Ewald for long-range electrostatics
pme_order        = 4                       ; cubic interpolation
fourierspacing   = 0.16                  ; grid spacing for FFT
; Temperature coupling is on
tcoupl                 = V-rescale         ; modified Berendsen thermostat
tc-grps                = Protein Non-Protein    ; two coupling groups - more accurate
tau_t                   = 0.1      0.1         ; time constant, in ps
ref_t                    = 300    300        ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl                = Parrinello-Rahman      ; Pressure coupling on in NPT
pcoupltype        = isotropic          ; uniform scaling of box vectors
tau_p                  = 2.0                    ; 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

Thanks in advance,

Akash