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. Thanks, Wes On Mon, Mar 23, 2020 at 3:54 AM Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > Hi > > On Sat, Mar 21, 2020 at 3:20 AM Wesley Michaels <wes.p.micha...@gmail.com> > wrote: > > > Hello, > > > > I hope this message finds you well! I'm running a pretty simple > simulation > > of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, > P = > > 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are exhibiting > > large, unstable volume fluctuations when I use the combination of the > > Parrinello-Rahman barostat and pairtype = 1 for 1-4 pairs. I don't see > this > > behavior with {PR barostat and pairtype = 2} or {Berendsen barostat and > > pairtype = 1}. > > > > I've specified the 1-4 pairs explicitly in the "[ pairs ]" section and > set > > "gen_pairs" to "yes" in the defaults section. I'm sure I'm missing > > something obvious, but here are the troubleshooting steps I've tried: > > > > > Sorry I could not understand the reason behind the modification you did. > Standard OPLS-AA force field field has "gen_pairs" to "yes" in > forcefield.itp and calculate the 1-4 interaction by uniformly scaling the > parameters. > No modifications are needed in the [pairs] section of the topol.top for > standard simulations with OPLS-AA. Or do you want to do something else? > See > > http://manual.gromacs.org/current/reference-manual/topologies/molecule-definition.html?highlight=pair > > to understand if your setting is inline which the force field. > > Best regards > > Alessandra > > > 1) ensure the simulation is equilibrated (up to 100 nanoseconds with > > Berendsen barostat beforehand, which is more than plenty I believe); > > 2) use a smaller time step (down to 0.01 fs); > > 3) increase the pressure coupling time constant (up to 10 ps); > > 4) using both GROMACS 2018 and GROMACS 2019. > > > > As far as energies go, I don't think there are worryingly large terms > that > > would blow the simulation up. Here's an example prepared with `gmx > energy`: > > Time (ps) Bond G96Angle RB LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Total > > Energy Conserved En. Volume Density > > 0 3.10E+04 5.40E+04 2.29E+04 8.76E+03 -1.66E+03 -4.71E+03 5.27E+03 > 2.17E+05 > > 2.17E+05 291.0 400.8 > > 2 5.11E+04 5.71E+04 8.24E+03 5.48E+02 -3.00E+03 -3.68E+03 9.01E+03 > 2.12E+05 > > 1.02E+06 3720.8 31.3 > > 4 2.56E+03 9.53E+03 8.18E+03 4.80E+03 -4.16E+03 -4.27E+03 9.40E+03 > 1.19E+05 > > 1.25E+06 21855.1 5.3 > > 6 4.76E+03 1.48E+04 1.15E+04 5.36E+03 -3.71E+03 -4.02E+03 8.68E+03 > 1.31E+05 > > 1.52E+06 88422.7 1.3 > > 8 6.58E+03 2.07E+04 1.48E+04 6.13E+03 -3.27E+03 -4.02E+03 7.95E+03 > 1.44E+05 > > 1.80E+06 246764.8 0.5 > > 10 1.05E+04 2.80E+04 1.64E+04 6.46E+03 -3.03E+03 -3.98E+03 7.61E+03 > > 1.57E+05 > > 2.08E+06 538599.2 0.2 > > > > > > Eventually, the volume becomes unphysically large and the density > extremely > > low. I'm sure I'm missing something obvious here (sorry for yet another > "my > > simulation is blowing up" question), so any insight into other steps I > > could try would be greatly appreciated. If I can provide any additional > > information (e.g. topology/mdp files), just let me know. > > > > Thanks, > > Wes > > -- > > 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.
