mirror of
https://github.com/microsoft/foldingdiff.git
synced 2026-06-04 13:30:33 +08:00
45 lines
2.5 KiB
Plaintext
45 lines
2.5 KiB
Plaintext
title = OPLS Lysozyme NPT equilibration
|
|
; define = -DPOSRES ; position restrain the protein
|
|
; Run parameters
|
|
integrator = md ; leap-frog integrator
|
|
nsteps = 50000 ; 2 * 50000 = 100 ps
|
|
dt = 0.002 ; 2 fs
|
|
; Output control
|
|
nstxout = 500 ; save coordinates every 1.0 ps
|
|
nstvout = 500 ; save velocities every 1.0 ps
|
|
nstenergy = 500 ; save energies every 1.0 ps
|
|
nstlog = 500 ; update log file every 1.0 ps
|
|
; Bond parameters
|
|
continuation = yes ; Restarting after NVT
|
|
constraint_algorithm = lincs ; holonomic constraints
|
|
constraints = h-bonds ; bonds involving H are constrained
|
|
lincs_iter = 1 ; accuracy of LINCS
|
|
lincs_order = 4 ; also related to accuracy
|
|
; Nonbonded settings
|
|
cutoff-scheme = Verlet ; Buffered neighbor searching
|
|
ns_type = grid ; search neighboring grid cells
|
|
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
|
|
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
|
|
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
|
|
DispCorr = EnerPres ; account for cut-off vdW scheme
|
|
; 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
|
|
; Velocity generation
|
|
gen_vel = no ; Velocity generation is off
|