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.abra...@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 <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. -- 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.