[gmx-users] Osmotic pressure
gozdeeergin at gmail.com
Fri Apr 15 12:00:34 CEST 2016
I use Berendsen for T and P-coupl.
Do you think I should change them?
> On 15 Apr 2016, at 11:55, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Also you can choose coupling algorithms that are known to sample correct
> On Fri, 15 Apr 2016 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
>>> 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
>>> 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
>> Roux paper? Are you remembering to divide by 2*area in your calculation
>> 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
>>> 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,
>>> 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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