[gmx-users] question about applying surface tension

[Ali Shomali]

Thanks so much Justin for your answer. actually I performed different
simulations and compared the area per lipid with existing studies . for
example I used gromacs charmm 22 for DPPC simulation and compared the
results with Dr.Feller's paper. also I conducted a simulation on DMPC
membrane and compared the results with existing data from
 doi:10.1021/jp048969n. also I performed a simulation with gromacs opls
force field on octadecanol monolayer and  checked the results with
 doi:10.1016/j.colsurfa.2012.09.025. in all of them my area per lipid value
changes very little and another odd thing is that even when I apply a large
surface tension , surface compresses!
I've tested all the option I could think of.
I would appreciate it so much  if you can help me with this problem Justin
thanks again
Ali

On Sun, May 7, 2017 at 10:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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