[gmx-users] Osmotic pressure
Justin Lemkul
jalemkul at vt.edu
Mon Apr 18 15:48:41 CEST 2016
On 4/18/16 4:43 AM, gozde ergin wrote:
> 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
Your fluctuation seems unreasonably low. Is this still with Berendsen? If so,
repeat it using Parrinello-Rahman for the barostat. This result should be quite
reproducible when using the method described exactly in the paper.
-Justin
>> 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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--
==================================================
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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