Hi, Also you can choose coupling algorithms that are known to sample correct ensembles...
Mark On Fri, 15 Apr 2016 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 > > -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 | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.