[gmx-users] Surface tension for water

[Iman Ahmadabadi]

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