[gmx-users] Osmotic pressure

[Mark Abraham]

Hi,

Are they known to produce these observables accurately? Might a wrong
distribution of KE affect them?

Mark

On Fri, 15 Apr 2016 12:00 gozde ergin <gozdeeergin at gmail.com> wrote:

> Hi Mark,
>
> 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:
> >
> > Hi,
> >
> > Also you can choose coupling algorithms that are known to sample correct
> > ensembles...
> >
> > Mark
> >
> > 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
> >> 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
> >>
> >> -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 | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >> --
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