Hello, This time I tried sesiisotropic scaling with Berendsen Barostat. The compressibility was set to zero in Z-direction allowing scaling only in X and Y. The NPT simulation was run for 10ns. The result did not look good and the average pressure was ~36 bar (reference pressure is 1 bar). Even more confusing was the graphs of various properties against time. Pressure vs time shows a sudden decrease in fluctuations at about 5ns and thereafter . The pressure fluctuations lowered to around ~170bar from ~650 bar. A dramatic change was observed in many properties at around this time. For eg, the short range LJ interaction was found to decrease sharply at ~5ns. Also, total energy, Kinetic, Potential energies and the temperature showed a rapid drop in the magnitude of their fluctuations from the same time.
Nothing notable was observed in the system trajectory at around this time. I am totally confused, and I feel that I made some very bad choice again the MDP file given below. Please let me know what you think. Suggest something on this issue which I should read about. ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 10000000 comm_mode = Linear nstcomm = 1 comm_grps = CHX SOL ; 7.3.8 Output Control nstxout = 25000 nstvout = 25000 nstfout = 25000 nstlog = 100 nstenergy = 100 nstxtcout = 100 xtc_precision = 1000 xtc_grps = System energygrps = System ; 7.3.9 Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb = 0.9 ; 7.3.11 VdW vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; 7.3.13 Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; 7.3.14 Temperature Coupling tcoupl = nose-hoover tc_grps = CHX SOL tau_t = 0.5 0.5 ref_t = 298 298 ; 7.3.15 Pressure Coupling pcoupl = berendsen pcoupltype = semiisotropic tau_p = 2.0 compressibility = 4.5e-5 0.0 ref_p = 1.0 1.0 ; 7.3.17 Velocity Generation gen_vel = no gen_temp = 298 gen_seed = -1 ; 7.3.18 Bonds constraints = none constraint_algorithm = LINCS continuation = no lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 Regards, Sujith. On Wed, Mar 12, 2014 at 5:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/12/14, 7:51 AM, sujithkakkat . wrote: > >> Hello, >> >> After a while I got back to the problem posted here. This issue was the >> large value for average pressure(~25 bar against the reference pressure >> of >> 1 bar) in NPT simulations with parrinello rahman barostat. The system >> studied is cyclohexane-water system with an interface. >> The forcefield is Gromos96. Gromacs 4.6.5 version is used. >> >> I recollect a post from Michael Shirts which says that with systems that >> are heterogeneous in direction (not uniform in x y and z), any errors in >> the pressure may be magnified. Is this what is happening in my case? >> >> Based on your suggestions , I tried the following to analyze/solve the >> problem, and till now the results have not improved a bit. >> >> (i) The system was simplified. Each phases was simulated separately. The >> results were good, with proper values of average pressure after NPT >> simulation for both independent water and cyclohexane systems. However, >> when doing the same with similar parameters on the water-cyclohexane >> combined system with parrinello-rahman barostat , still gives very high >> average pressure (even after 10ns ) >> >> (ii) Changing the tau_p values did not help either. (I tried 1ps, 2ps, >> and 4ps) >> >> My question is whether, I can try the semiisotropic scaling? The manual >> says that it is useful in case of systems with interface. I am not sure, >> since none of the replies I got suggested that option, which gives the >> impression that it is not the best solution. But , to my limited knowledge >> that is the only option left to be tried to solve the issue. >> >> > Worth a shot. Also try changing the barostat to Berendsen to see if that > changes anything. There are a lot of interrelated issues here, possibly a > problem with the barostat, the tau_p value, the type of coupling, the > combination of the integrator and barostat...you see how complicated it > gets, and that's only some of the possible issues. > > -Justin > > > >> The mdp file used is, >> >> ; 7.3.3 Run Control >> integrator = md >> tinit = 0 >> dt = 0.001 >> nsteps = 10000000 >> comm_mode = Linear >> nstcomm = 1 >> comm_grps = CHX SOL >> >> ; 7.3.8 Output Control >> nstxout = 25000 >> nstvout = 25000 >> nstfout = 25000 >> nstlog = 100 >> nstenergy = 100 >> nstxtcout = 100 >> xtc_precision = 1000 >> xtc_grps = System >> energygrps = System >> >> ; 7.3.9 Neighbor Searching >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> rlist = 0.9 >> >> ; 7.3.10 Electrostatics >> coulombtype = PME >> rcoulomb = 0.9 >> >> ; 7.3.11 VdW >> vdwtype = cut-off >> rvdw = 1.4 >> DispCorr = EnerPres >> >> ; 7.3.13 Ewald >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> >> ; 7.3.14 Temperature Coupling >> tcoupl = nose-hoover >> tc_grps = CHX SOL >> tau_t = 0.5 0.5 >> ref_t = 298 298 >> >> ; 7.3.15 Pressure Coupling >> pcoupl = parrinello-rahman >> pcoupltype = isotropic >> tau_p = 2.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> >> >> ; 7.3.17 Velocity Generation >> gen_vel = no >> gen_temp = 298 >> gen_seed = -1 >> >> ; 7.3.18 Bonds >> constraints = none >> constraint_algorithm = LINCS >> continuation = no >> lincs_order = 4 >> lincs_iter = 1 >> lincs_warnangle = 30 >> >> >> >> Please comment. >> >> Sujith. >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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? 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