[gmx-users] Osmotic pressure
gozde ergin
gozdeeergin at gmail.com
Mon Apr 18 10:43:04 CEST 2016
In Roux study they did 10 independent 1.5 ns production simulation and I did 15 ns simulation and divided it to 10 1.5ns simulations.
Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
Roux study 300 (+/- 10 bar)
Experiment 300 bar
> On 18 Apr 2016, at 10:29, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> Hi,
>
> What statistical error do you (and they) measure? How many replicates have
> each of you done?
>
> Mark
>
> On Mon, 18 Apr 2016 10:25 gozde ergin <gozdeeergin at gmail.com> wrote:
>
>> Hi Justin,
>>
>> I corrected the nonbonded settings as your suggestion ;
>>
>> ; Bond parameters
>> continuation = no
>> constraint_algorithm = shake
>> constraints = h-bonds
>> shake_tol = 0.0001
>> cutoff-scheme = Verlet
>> vdwtype = cutoff
>> vdw-modifier = force-switch
>> rvdw-switch = 1.0
>> ; Neighborsearching
>> ns_type = grid
>> nstlist = 5
>> rlist = 1.2
>> rcoulomb = 1.2
>> rvdw = 1.2
>>
>> However my osmotic pressure result is still far from the Luo&Roux 2010
>> study.
>> I have the same number of Na Cl ions and water molecules. I run the
>> simulation for 15ns.
>> System size is the same, water model and force field are the same as Roux
>> study.
>> Basically I should get the same result.
>> Here is the result,
>>
>> Osmotic pressure for 5M : My result 217 bar
>> Roux study ~300 bar
>>
>> Any suggestions would be appreciated.
>>
>>> 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>
>>>
>>> -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 <mailto:
>> jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul <
>> http://mackerell.umaryland.edu/~jalemkul>
>>>
>>> ==================================================
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