[gmx-users] Surface tension for water

[Iman Ahmadabadi]

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