[gmx-users] Periodic Cell of Cyclohexane--LINCS Warnings

[Billy Williams-Noonan]

Hi Experts,

When running a simulation of cyclohexane in a periodic cell (constructed
such that the density is 0.779 g/mL) the simulation crashes during the
final 10 ns equilibration phase using Parrinello-Rahman as the barostat.
Changing the time-step to 1 fs fixes this problem.  Using a Berendsen does
not lead to this issue.  Additionally, increasing tau_p to 6 ps with the
Parrinello-Rahman barostat, also fixes this problem.

I'm leaning toward the final solution, but I am wondering if this is a
reasonable thing to do.  I have read the Gromacs manual describing the
mathematics behind the Parrinello-Rahman barostat, and I have read the mdp
settings page for Gromacs.

It is still unclear to me whether increasing tau_p would affect the
simulation negatively at all, especially since it had been pre-equilibrated
with Berendsen (2 fs time-step) and Parrinello-Rahman (1 fs) for 10 ns in
separate runs before this run (tau_p is 6).

Any advice would be appreciated :)

Many Thanks,

Billy

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