[gmx-users] question about applying surface tension

[Justin Lemkul]

On 5/6/17 6:58 PM, Ali Shomali wrote:
> 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

Sounds like a force field issue.  Which parameter set are you using, and do you 
have evidence that it should respond correctly under such conditions?

-Justin

>  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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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