[gmx-users] Surface tension for water

[Iman Ahmadabadi]

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