[gmx-users] How to fix interfacial tension in NPT

[Souilem Safa]

Dear Justin,
Thank you for your answer, I'm sorry for delay to reply. Actually I'm
running a simulation of oil-water interface. I'm using Gromos 53a6 force
field which is usually used for triglycerides. after semiisotropic and MD
step I still have around 40 mN.m-1 interfacial tension which is pretty far
from my experimental value. Following is my mdp file for NPT step.
I would be very grateful if you can help me to solve this issue
title           = NPT equilibration
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 250000        ; 2 *250000 = 500 ps
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 500           ; save coordinates every 1 ps
nstvout         = 100           ; save velocities every 0.2 ps
nstenergy       = 100           ; save energies every 0.2 ps
nstlog          = 100           ; 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      = 2             ; accuracy of LINCS
lincs_order     = 2             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
; 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         = SOL TRI       ; 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      = semiisotropic         ; uniform scaling of box vectors
tau_p           = 1.0 1.0               ; time constant, in ps
ref_p           = 1.0 1.0               ; reference pressure, in bar
compressibility = 0   4.5e-5    ; isothermal compressibility x,y axis/z
axis bar^-1
refcoord_scaling = com
; 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




On 19 April 2013 03:28, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/18/13 10:51 AM, Souilem Safa wrote:
>
>> Dear Gromacs users,
>> I have runned a semiisotropic NPT simulation for a membrane, I have fixed
>> the pressure in x and y axis and I varied it only in z axis to keep a
>> stable interface. But after simulation the obtained interfacial tension is
>> far bigger than the experimental value. Experimental is 27 mN.m-1 and the
>> simulated one was around 38 mN.m-1.
>> I will be very grateful if you can suggest me which parameters should I
>> check in order to regulate the interfacial tension value.
>>
>
> You haven't posted your .mdp file or even stated what force field you're
> using.  Is your force field designed to reproduce such surface tension
> values?  The results are only as good as the model itself, and your usage
> of it.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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