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

[Justin Lemkul]

On 4/21/13 9:30 PM, Souilem Safa wrote:
> 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

Do you have any reason to believe that 53A6 should reproduce quantities like 
surface tension?  I haven't seen such a demonstration before, though I admit I 
haven't actively gone looking.  The cutoffs you are using are incorrect for 
strict use of 53A6; that could be a contributing factor to your problems.

-Justin

> 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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-- 
========================================

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

========================================