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

[Mark Abraham]

Hi,

On Mon, Jun 12, 2017 at 12:27 PM Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> Also, the topology for the cyclohexane comes from the ATB and looks very
> reasonable.
>
> On 12 June 2017 at 20:25, Billy Williams-Noonan <
> billy.williams-noonan at monash.edu> wrote:
>
> > 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


Side issue, not related to your problem - use gmx grompp -t state.cpt to
get the full-precision coordinates and box.

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.
>

P-R isn't stable with respect to volume changes (tends to start to
oscillate, leading to crazy forces, which breaks LINCS), which is why I
suggested you look at your volumes. Just picking a random length of time
isn't a good methodology ;-) When I use P-R, I choose time constants in the
range of 5-10 ps, but I don't know what happens when you choose a smaller
number and some aspect of the simulation can't tolerate that.

Mark


> > 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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> >> >
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> >
> >
> >
> > --
> > Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
> >
> > *LinkedIn Profile
> > <
> http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button
> >
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> >
> > Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> > Royal Parade, Parkville, 3052
> >
> >
>
>
> --
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>
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> >
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