[gmx-users] Osmotic pressure

[gozde ergin]

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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