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 <nedoma...@gmail.com> 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 <jwi...@uwyo.edu> 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? 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.