[gmx-users] Osmotic pressure
jalemkul at vt.edu
Fri Apr 15 11:50:28 CEST 2016
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.
> ; 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 | (410) 706-7441
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