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.abra...@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 <gozdeeer...@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 <jalem...@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 >>> >>> jalem...@outerbanks.umaryland.edu <mailto: >> jalem...@outerbanks.umaryland.edu> | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul < >> http://mackerell.umaryland.edu/~jalemkul> >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List < >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before >> posting! >>> >>> * Can't post? 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