The point is that any metastable state in numerical simulations requires fine-tuned Hamiltonians.
On Fri, May 1, 2015 at 2:47 PM, Alex <[email protected]> wrote: > With opls-aa, incorrect densities and diffusivities were calculated entirely > away from the critical point for several liquids. > > Alex > > On May 1, 2015 11:40 AM, "V.V.Chaban" <[email protected]> wrote: >> >> This problem is natural. Even small change in (T,P) in the >> supercritical range results in a huge change of density and, hence, >> all other properties. >> >> You need either to alter (T,P) or to adjust the force field model >> (both change will be slight, but will bring large changes of density). >> >> If you expect any phase separation in these setups, take care of the >> Gibbs rule. >> >> >> >> >> On Thu, Apr 30, 2015 at 6:38 PM, Alex <[email protected]> wrote: >> > Only other suggestion I have is that 5 ns production runs are probably >> > not >> > long enough. Granted, we needed diffusion data, so I believe I had 50 to >> > 100 ns long simulations, but even for the barostat to settle, it may be >> > a >> > good idea to have simulations significantly longer than 5 ns. >> > >> > Alex >> > >> > On Thu, Apr 30, 2015 at 3:14 PM, Alex <[email protected]> wrote: >> > >> >> Unfortunately, I had a pretty terrible experience trying to simulate >> >> fuels, fuel mixtures, and CO2 dissolved in fuels with Gromacs (using >> >> OPLS-AA) at high pressures and/or temperatures. It is my understanding >> >> that >> >> at the moment this is isn't the area where these forcefields are >> >> seriously >> >> tested. >> >> >> >> I have no results for other forcefields, but for OPLS-AA it was >> >> unpublishable and came out as an internal note at the institution. If >> >> curious, see >> >> http://nvlpubs.nist.gov/nistpubs/TechnicalNotes/NIST.TN.1805.pdf >> >> In fact, if you get any results that correspond to experimental data, >> >> I'll >> >> really appreciate it if you let me know. :) >> >> >> >> Alex >> >> >> >> On Thu, Apr 30, 2015 at 2:04 PM, Jarrett Lee Wise <[email protected]> >> >> wrote: >> >> >> >>> Hello all- >> >>> >> >>> I am trying to run simulations containing supercritical CO2 and oil >> >>> asphaltenes. I have tested various force fields (TraPPE flex, TraPPe >> >>> rigid, Charmm, EPM2, Cygan, and Zhang), but all of my results give >> >>> either >> >>> extremely low densities (~200 kg/m^3) or extremely high densities >> >>> (~1600 >> >>> kg/m^3) when the density should be around 630 kg/m^3. >> >>> >> >>> >> >>> I equilibrated a system of 5000 CO2 molecules with Nose-Hoover and >> >>> Berendsen for 5 ns, then did a production run using Nose-Hoover and >> >>> Parrinello-Rahman for another 5 ns using 1 fs time step. >> >>> >> >>> I have found that tau_p plays an important factor. A relaxed tau_p >> >>> gives >> >>> low density while a vigorous tau_p gives a high density and crashes >> >>> using >> >>> Parrinello-Rahman pressure coupling. >> >>> >> >>> >> >>> Has anyone else encountered similar problems or have any advice? >> >>> >> >>> Here is a copy of my MDP file. Any advice is greatly appreciated. >> >>> >> >>> Thanks >> >>> >> >>> >> >>> Jarrett Wise >> >>> PhD Student >> >>> Petroleum Engineering >> >>> University of Wyoming >> >>> >> >>> >> >>> title = CO2 Density Run >> >>> integrator = md >> >>> nsteps = 5000000 >> >>> dt = 0.001 >> >>> nstxout = 0 >> >>> nstvout = 0 >> >>> nstfout = 0 >> >>> nstxtcout = 20000 >> >>> nstenergy = 100 >> >>> nstlog = 1500 >> >>> >> >>> constraint_algorithm = lincs >> >>> constraints = H-Bonds >> >>> lincs_iter = 1 >> >>> lincs_order = 4 >> >>> >> >>> cutoff-scheme = Verlet >> >>> ns_type = grid >> >>> nstlist = 100 >> >>> rlist = 1.4 >> >>> rcoulomb = 1.4 >> >>> rvdw = 1.4 >> >>> nstcalcenergy = 10 >> >>> comm_mode = linear >> >>> >> >>> coulombtype = PME >> >>> pme_order = 4 >> >>> fourierspacing = 0.16 >> >>> >> >>> tcoupl = Nose-Hoover >> >>> tc-grps = System >> >>> tau_t = 5.0 >> >>> ref_t = 320 >> >>> >> >>> >> >>> pcoupl = Parrinello-Rahman >> >>> pcoupltype = isotropic >> >>> tau_p = 3.0 >> >>> ref_p = 520.0 >> >>> compressibility = 1.45e-4 >> >>> >> >>> pbc = xyz >> >>> continuation = yes >> >>> gen_vel = no >> >>> gen_temp = 320 >> >>> >> >>> >> >>> -- >> >>> 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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