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
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