[gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities

Wesley Michaels wes.p.michaels at gmail.com
Tue Mar 24 08:09:53 CET 2020


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.biosim at gmail.com> wrote:

> Hi
>
> On Sat, Mar 21, 2020 at 3:20 AM Wesley Michaels <wes.p.michaels at 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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