On 4/21/13 9:30 PM, Souilem Safa wrote:
Dear Justin,
Thank you for your answer, I'm sorry for delay to reply. Actually I'm
running a simulation of oil-water interface. I'm using Gromos 53a6 force
field which is usually used for triglycerides. after semiisotropic and MD
step I still have around 40 mN.m-1 interfacial tension which is pretty far
from my experimental value. Following is my mdp file for NPT step.
I would be very grateful if you can help me to solve this issue
Do you have any reason to believe that 53A6 should reproduce quantities like
surface tension? I haven't seen such a demonstration before, though I admit I
haven't actively gone looking. The cutoffs you are using are incorrect for
strict use of 53A6; that could be a contributing factor to your problems.
-Justin
title = NPT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 250000 ; 2 *250000 = 500 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = yes ; Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 2 ; accuracy of LINCS
lincs_order = 2 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = SOL TRI ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl = parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of box vectors
tau_p = 1.0 1.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, in bar
compressibility = 0 4.5e-5 ; isothermal compressibility x,y axis/z
axis bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = enerpres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
On 19 April 2013 03:28, Justin Lemkul <jalem...@vt.edu> wrote:
On 4/18/13 10:51 AM, Souilem Safa wrote:
Dear Gromacs users,
I have runned a semiisotropic NPT simulation for a membrane, I have fixed
the pressure in x and y axis and I varied it only in z axis to keep a
stable interface. But after simulation the obtained interfacial tension is
far bigger than the experimental value. Experimental is 27 mN.m-1 and the
simulated one was around 38 mN.m-1.
I will be very grateful if you can suggest me which parameters should I
check in order to regulate the interfacial tension value.
You haven't posted your .mdp file or even stated what force field you're
using. Is your force field designed to reproduce such surface tension
values? The results are only as good as the model itself, and your usage
of it.
-Justin
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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