[gmx-users] question about applying surface tension

Ali Shomali ali.shomali111 at gmail.com
Sun May 7 00:58:32 CEST 2017


Hello to all dear gromacs users

I've faced a problem with applying surface tension , I'm , trying to model
a monolayer and I've noticed whenever I apply a surface tension although my
surface tension is converged  my area per lipid is wrong . i managed to
model a bilayer to find out the problem and i noticed that in all my
simulations my area per lipid changes are very little no matter what is
surface tension nor cutoffs. but surface tension converges! i'm sending my
mdp file .
I will be so thankful if some one helps
 mdp file :

title = DMPC NPT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 1000000 ; = 1000 ps
dt = 0.001 ; 1 fs
nstcomm                  = 10
comm-grps                = SOL DMPC ; Remove COM for monolayers separately
; Output control
nstxout = 10000 ; save coordinates every 1.0 ps
nstvout = 10000 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps

; Neighborsearching
cutoff-scheme   = Verlet
ns_type     = grid ; search neighboring grid cells
nstlist     = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb     = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw     = 1.4 ; short-range van der Waals cutoff (in nm)
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype     = PME ; Particle Mesh Ewald for long-range electrostatics
; Temperature coupling is on
tcoupl = berendsen             ; modified Berendsen thermostat
tc-grps = DMPC SOL ; two coupling groups - more accurate
tau_t = 0.1   0.1           ; time constant, in ps
ref_t = 330    330           ; reference temperature, one for each group,
in K
; Pressure coupling is on
Pcoupl = berendsen
tau_p = 10.0
compressibility = 4.5e-5 4.5e-5
ref_p = 600 1.0
; Periodic boundary conditions
pbc = xyz     ; 3-D PBC


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