[gmx-users] Surface tension for water

[Dan Gil]

Iman,

You get the error message in the terminal if you are running it on your own
machine. If you are running on a supercomputer, the error messages will be
directed to a file. How do you know the simulation is crashing without the
software telling you? Please find the message (check all outputs), wherever
it might be, and share it with us. Otherwise I don't know what the problem
could be.

Dan

On Tue, Aug 29, 2017 at 4:14 PM, 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
> --
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