[gmx-users] appropriate tau-p for surface tension coupling
Ali Shomali
ali.shomali111 at gmail.com
Sun May 28 16:25:48 CEST 2017
Hello to all dear gromacs users
I'm simulating a monolayer using pcouple= surface tension and as manual
says my converged area per lipid and surface tension are very much
dependable on the value of tau-p , so can some one help me how can I make
sure that my tau-p value is OK?
thanks
Ali
mdp script:
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000000 ; (10 ns)
dt = 0.001 ; 1 fs
; Output control
nstxout = 100000 ; save coordinates every 0.2 ps
nstvout = 100000 ; save velocities every 0.2 ps
nstenergy = 500 ; save energies every 0.2 ps
nstlog = 1000 ; 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
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cels
nstlist = 10 ; 10 fs
rlist = 1.4 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
vdwtype = Cut-off
; Temperature coupling is on
tcoupl = berendsen ; More accurate thermostat
tc-grps = SOL OCT ; three coupling groups - more accurate
tau_t = 0.5 0.5 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = berendsen ; Pressure coupling on in NPT
pcoupltype = surface-tension ; uniform scaling of x-y box vectors,
independent z
tau_p = 1.0 1.0 ; time constant, in ps
ref_p = 800 1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5 0 ; isothermal compressibility, bar^-1
; 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
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 10
comm-mode = Linear
comm-grps = SOL OCT
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