[gmx-users] Osmotic pressure
gozdeeergin at gmail.com
Fri Apr 15 11:58:03 CEST 2016
Justin thank you very much for your quick respond. These values that I get, for ideal solution and in Roux paper are shown below ;
Osmotic pressure for 3M : My result 156 bar
Ideal solution 150 bar
Roux study ~155 bar
Osmotic pressure for 4M : My result 194 bar
Ideal solution 200 bar
Roux study ~220 bar
Osmotic pressure for 5M : My result 251 bar
Ideal solution 250 bar
Roux study ~300 bar
Yes I divide in two for two walls. Ok I rerun the simulation with these new settings.
Thanks a lot.
> 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>
>> ; 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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