[gmx-users] Osmotic pressure
Mark Abraham
mark.j.abraham at gmail.com
Mon Apr 18 10:29:31 CEST 2016
Hi,
What statistical error do you (and they) measure? How many replicates have
each of you done?
Mark
On Mon, 18 Apr 2016 10:25 gozde ergin <gozdeeergin at gmail.com> wrote:
> 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 <jalemkul at 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
> >
> > jalemkul at outerbanks.umaryland.edu <mailto:
> jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul <
> http://mackerell.umaryland.edu/~jalemkul>
> >
> > ==================================================
> > --
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