Hi Justin,
I corrected the nonbonded settings as your suggestion ;
; Bond parameters
continuation = no
constraint_algorithm = shake
constraints = h-bonds
shake_tol = 0.0001
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
However my osmotic pressure result is still far from the Luo&Roux 2010
study.
I have the same number of Na Cl ions and water molecules. I run the
simulation for 15ns.
System size is the same, water model and force field are the same as Roux
study.
Basically I should get the same result.
Here is the result,
Osmotic pressure for 5M : My result 217 bar
Roux study ~300 bar
Any suggestions would be appreciated.
On 15 Apr 2016, at 11:50, Justin Lemkul <jalem...@vt.edu> wrote:
On 4/15/16 5:20 AM, gozde ergin wrote:
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.
What values do you actually get? How do they compare with the values
from the Roux paper? Are you remembering to divide by 2*area in your
calculation (since you have two walls)?
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 ;
These nonbonded settings are wrong. The values for CHARMM36 are well
established and you should not deviate from them.
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM <
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM>
-Justin
; 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
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu <mailto:
jalem...@outerbanks.umaryland.edu> | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul <
http://mackerell.umaryland.edu/~jalemkul>
==================================================
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