[gmx-users] Surface tension for water

André Farias de Moura moura at ufscar.br
Wed Aug 30 15:50:18 CEST 2017


I cannot understand the point of performing NPT coupling to compute surface
tension, the usual approach relies on NVT simulations instead. You might
want to take a look at this very nice investigation of the surface tension
of many water models (all done using GROMACS at constant NVT conditions):

http://rabida.uhu.es/dspace/bitstream/handle/10272/9574/Surface_tension.pdf?sequence=2

In principle, you could couple the lateral pressure to an external bath
with the exact surface tension of your model, then mechanical equilibrium
should be attained, but pressure varies wildly during MD simulations, so
actual mechanical equilibrium might not happen so easily (it seems to be
your case)

besides, your are coupling to the experimental surface tension of water,
whereas any water model has a different surface tension (usually smaller
than the experimental value). If you couple your system to a lateral
surface tension much different from what should be its equilibrium surface
tension during an MD simulation, then you are in fact applying a net
lateral pressure different from zero and again I guess this is why you are
getting your simulations crashing with high T and P values.

So unless you have a very clear idea of why you might want to perform that
simulation with a surface tension coupling, I would strongly suggest you to
use NVT instead.

IMNSHO surface tension coupling only makes sense if the liquid (whether
water or any other subphase you might be interested in) can support a
insoluble (or at least poorly soluble) film on each interface (film meaning
either monolayers, bilayers, multilayers or just another immiscible
liquid, maybe a solid state too, depending on P and T range).

I hope it helps

Andre

On Wed, Aug 30, 2017 at 2:26 AM, Iman Ahmadabadi <imanahmadabadi75 at gmail.com
> wrote:

> Dear Dan,
>
> As you can see in the images I sent to you, there is no error massage in
> output files. The properties of the system such as pressure or temperature
> is so high, that's why I've concluded that the system is crashed.
>
> Sincerely,
> Iman
>
> On Wed, Aug 30, 2017 at 12:44 AM, Iman Ahmadabadi <
> imanahmadabadi75 at gmail.com> wrote:
>
> > Hi Dan,
> >
> > There is no error massage, It's just a crashing and stopping the
> > simulation. The version is 4.6.0.
> >
> > Iman
> >
> > On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi <
> > imanahmadabadi75 at gmail.com> wrote:
> >
> >> Dear Dan,
> >>
> >> I have attached the NPT.mdp file in the following:
> >>
> >> title =  NPT equilibration
> >> ; Run parameters
> >> integrator = md
> >> nsteps = 20000000
> >> dt    = 0.001
> >>
> >> ; Output control
> >> nstxout = 500
> >> nstvout = 500
> >> nstenergy = 500
> >> nstlog = 500
> >>
> >> ; Bond parameters
> >> continuation        = no
> >> constraint_algorithm    = lincs
> >> constraints            = all-bonds
> >> lincs_iter            = 1
> >> lincs_order            = 4
> >>
> >> ; Neighborsearching
> >> cutoff-scheme   = Verlet
> >> ns_type    = grid
> >> nstlist    = 20
> >> rlist               = 2.0
> >> rcoulomb    = 2.0
> >> rvdw    = 2.0
> >>
> >> ; Electrostatics
> >> coulombtype    = PME
> >> pme_order    = 4
> >> fourierspacing = 0.12
> >>
> >> ; Temperature coupling is on
> >> tcoupl = V-rescale
> >> tc-grps = system
> >> tau_t = 0.1
> >> ref_t = 298.15
> >>
> >> ; Pressure coupling is on
> >> pcoupl        = berendsen
> >> pcoupltype        = surface-tension
> >> tau_p        = 2.0  2.0
> >> ref_p        = 1440  1.0
> >> compressibility         = 4.46e-5  0
> >> refcoord_scaling        = com
> >>
> >> ; Periodic boundary conditions
> >> pbc = xyz
> >>
> >> ; Dispersion correction
> >> DispCorr = EnerPres
> >>
> >> ; Velocity generation
> >> gen_vel = yes
> >> lincs_warnangle = 90
> >>
> >>
> >> Now I'm gonna using semiisotropic instead of surface tension like in the
> >> following:
> >> pcoupltyp       = semiisotropic
> >> tau_p         = 0.5
> >> ref_p                      = 1.0  1.0
> >> compressibility         = 4.46e-5  0
> >>
> >> Thank you for your help.
> >> Sincerely,
> >> Iman
> >>
> >> On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi <
> >> imanahmadabadi75 at gmail.com> wrote:
> >>
> >>> Dear All Users,
> >>>
> >>> I'm calculating the surface tension of the water, my box contains
> almost
> >>> 5000 water molecule in the middle of that. Through NVT equilibration,
> I got
> >>> reasonable results for surface tension but when I use NPT for my
> system,
> >>> the system crashes every time. The pressure coupling options are in the
> >>> following:
> >>>
> >>> pcoupltyp                 = surface-tension
> >>> tau_p        = 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
> >>> three values)
> >>> ref_p                      = 1440  1.0
> >>> compressibility         = 4.46e-5  0
> >>>
> >>> first ref-p value is 720*2 = 1440. 720 is the surface tension of water
> >>> in 298.15.
> >>>
> >>> Now, I'm going to use semiisotropic for P-coupling:
> >>>
> >>> pcoupltyp       = semiisotropic
> >>> tau_p         = 0.5
> >>> ref_p                      = 1.0  1.0
> >>> compressibility         = 4.46e-5  0
> >>>
> >>> Could I have any recommendation about my problem with surface-tension
> >>> pcoupltyp? Am I right with semiisotropic options?
> >>>
> >>>
> >>> Respectfully,
> >>> Iman Ahmadabadi
> >>>
> >>
> >>
> >>
> >> --
> >> Iman Ahmadabadi
> >>
> >> Sharif University of Technology, Tehran, Iran
> >>
> >> Department of Physics and Chemistry
> >>
> >> Phone: (+98) 9156125273
> >>
> >> Email: Imanahmadabadi75 at gmail.com , ahmadabadi_i at ch.sharif.edu
> >>
> >
> >
> >
> > --
> > Iman Ahmadabadi
> >
> > Sharif University of Technology, Tehran, Iran
> >
> > Department of Physics and Chemistry
> >
> > Phone: (+98) 9156125273
> >
> > Email: Imanahmadabadi75 at gmail.com , ahmadabadi_i at ch.sharif.edu
> >
>
>
>
> --
> Iman Ahmadabadi
>
> Sharif University of Technology, Tehran, Iran
>
> Department of Physics and Chemistry
>
> Phone: (+98) 9156125273
>
> Email: Imanahmadabadi75 at gmail.com , ahmadabadi_i at ch.sharif.edu
> --
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090


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