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

[Mark Abraham]

Hi,

On Mon, Jun 12, 2017 at 11:21 AM Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> 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.
>

Looks like some of the integration setups are more stable than others. What
is the volume doing during these runs? What does P-R 2fs do after a stage
of P-R 1fs?


> 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 :)
>

It's normal to use tau-p around a factor of 10 larger for P-R than
Berendsen. They work in fundamentally different ways.

I would also check whether your non-bonded scheme is consistent with
general practice for that forcefield in GROMACS (it may be, I just don't
know).

Mark

Many Thanks,
>
> Billy
>
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