[gmx-users] UMBRELLA SAMPLING

[Subashini .K]

Hi gromacs users,


I want to perfom NVT equilibration, pull code (using pull-geometry = direction-periodic)


Prior to this step, energy minimization (500 steps) and NPT equilibration (50000 steps) was done


As I am new to gromacs and simulations, can anyone tell me whether the following NVT code is correct?


Is this code for NVT correct?


title = Umbrella pulling simulation
define = -DPOSRES
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 50000 ; 100 ps
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc_grps = Protein Non-Protein
tau_t = 0.5 0.5
ref_t = 310 310
; Pressure coupling is off
Pcoupl = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Velocity generation
gen_vel = no ;

; Pull code

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Thanks,
Subashini.K