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

[Billy Williams-Noonan]

Thanks for your reply, Mark (Professor Abraham?)

"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?"

P-R is Parrinello-Rahman? 10 ns equilibration ends without any signs of
problems with the 1 fs timestep.  I then took the gro file from that
equilibration and re-equilibrated for 10 ns using P-R.  Did not last more
than 5 ns each time.  System is stable with Berendsen using a 2 fs
time-step.

"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)."

Thank you :)

I guess my question is then, should my system be crashing using P-R with a
2 fs timestep and tau_p being 2 ps.  Increasing to 6 ps and leaving the
time-step constant at 2 ps seems to fix the problem.

Cheers,

Billy





On 12 June 2017 at 20:05, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> 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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-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052