Hey y'all, Ran some additional simulations and, unfortunately, I'm still experiencing problems. Here's the mdp file that I used:
integrator = md nsteps = 20000000 ; 20 ns dt = 0.001000 nstlist = 20 ns_type = grid nstxout = 25000 nstvout = 25000 nstenergy = 25000 nstlog = 25000 continuation = yes constraints = none lincs_iter = 1 lincs_order = 4 cutoff-scheme = Verlet rcoulomb = 1.4 rvdw = 1.4 coulombtype = PME vdwtype = PME pme_order = 4 fourierspacing = 0.12 tcoupl = Nose-Hoover tc-grps = System tau_t = 0.100000 ref_t = 300.000000 nsttcouple = 5 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.000000 ref_p = 1.000000 compressibility = 0.000045 refcoord_scaling = com pbc = xyz periodic-molecules = no DispCorr = EnerPres gen_vel = no The simulation ran for 40ns with the Berendsen barostat just fine - density and volume were well-equilibrated within 1ns of the simulation starting. Unstable density fluctuations began immediately after switching to the PR barostat (from the output configuration of the previous 40ns run) and the simulation failed within 0.4ns. Here are some links to: - topology file: https://drive.google.com/open?id=1NF5EPbM2mnTGilXpOf7pQK5qlelBd8KC - initial configuration: https://drive.google.com/file/d/1kxMOKQcsAEheBCEAbkGcXqfBDwsHKpwr/view?usp=sharing - log file of second half of Berendsen run: https://drive.google.com/file/d/15TgbOOr6_fb8FkqR-nFHR8j1qbhTNT-Q/view?usp=sharing - log file of PR run: https://drive.google.com/file/d/1CPobb3ddDsd4I6Fce1tEpwHiBd5yq-tE/view?usp=sharing Thanks! If you need any other files or information, please let me know. -Wes On Tue, Mar 24, 2020 at 3:44 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/24/20 3:09 AM, Wesley Michaels wrote: > > Hi, > > > > Thanks for your reply! I built the topology with my own script, as > opposed > > to using pdb2gmx. Following Bogdan's instructions here ( > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html > ), > > I specified all instances of 1-4 pair interactions (i.e. pairs of atom > > indices) in the [ pairs ] section, but let GMX specify the [ pairtypes ] > > section (i.e. the interaction parameters for pairs of atom types) > > automatically using "gen_pairs" = "yes". > > > > As a second test, I generated a topology using pdb2gmx and the procedure > > Justin detailed here ( > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html > ) > > (using the OPLS-AA FF option in pdb2gmx) and used that in a trial > > simulation. I experienced the same issue, unfortunately. Happy to provide > > any files as needed to help clarify the issue. > > If pdb2gmx built the topology and you're using an unaltered > forcefield.itp [defaults] directive, based on what you've said below, it > appears to just be an equilibration issue. Use Berendsen for a while to > get the system settled and then switch to Parrinello-Rahman. If you're > still experiencing problems, full .mdp file(s) would be helpful. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.
