[gmx-users] Osmotic pressure
gozde ergin
gozdeeergin at gmail.com
Fri Apr 15 11:20:18 CEST 2016
Dear all,
I simulate the NaCl solution to estimate the osmotic pressure. My salt concentrations are 3,4 and 5M. I apply flat-bottom restraint to the molecules.
I use CHARMM36 ff with NBFIX correction.
After the simulation I extract the z-coordinates of restraint ions and use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic pressure.
Actually I try to get the similar results as Lou&Roux 2010 study.
However my osmotic pressure results are on the line of ideal solution osmotic pressure as shown equation in below;
P = cRT (Van’t Hoff equation)
but not the similar result with experiments.
Is there anyone here that get the same trend as me for osmotic pressure calculation? Or is there something that I miss?
Here is my .mdp file;
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 2500000 ;
; Output control
nstxout = 2000
nstvout = 2000
nstlog = 2000
nstenergy = 2000
; Bond parameters
continuation = no ;
constraint_algorithm = shake ; h
constraints = all-bonds ; a
shake_tol = 0.0001
; Neighborsearching
ns_type = grid ;
nstlist = 5 ;
rlist = 1.1 ;
rcoulomb = 1.1 ;
rvdw = 1.1 ;
; Electrostatics
coulombtype = PME ;
pme_order = 4 ;
fourierspacing = 0.16 ;
tcoupl = berendsen
tc-grps = System
tau_t = 1.0
ref_t = 300
; Pressure coupling is on
pcoupl = Berendsen ; Pressure coupling on in NPT, also weak coupling
pcoupltype = semiisotropic ; uniform scaling of x-y-z box vectors
tau_p = 2.0 2.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure (in bar)
compressibility = 0 4.5e-5 ; isothermal compressibility, 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 = yes ; Velocity generation is on
gen_temp = 300 ; temperature for velocity generation
gen_seed = -1 ; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode = Linear
comm-grps = System
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