[gmx-users] strange behaviout in 5.1.2
Mark Abraham
mark.j.abraham at gmail.com
Fri Feb 5 23:16:09 CET 2016
Hi,
Thanks. I did make a config change yesterday that might be the cause. I'll
revert the config if the issues persist tomorrow.
Mark
On Fri, Feb 5, 2016 at 11:12 PM Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:
> Never mind. My review went through anyway.
>
> > On 5 Feb 2016, at 22:11, Erik Marklund <erik.marklund at chem.ox.ac.uk>
> wrote:
> >
> > Am trying to review this, but the gerrit interface keeps complaining
> about a “500 Internal server error”.
> >
> > Kind regards,
> > Erik
> >
> >> On 5 Feb 2016, at 17:59, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> >>
> >> Hi,
> >>
> >> Docs amended at https://gerrit.gromacs.org/5618 :-)
> >>
> >> Mark
> >>
> >> On Fri, Feb 5, 2016 at 6:26 PM Mark Abraham <mark.j.abraham at gmail.com>
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> You're reading readir.c correctly, and it is correct also. I was
> >>> mis-reading
> >>>
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html
> about
> >>> semiisotropic coupling. (I guess you could imagine that you might want
> >>> different tau-p for semiisotropic coupling, but it's definitely not
> >>> implemented.)
> >>>
> >>> I agree that it is irritating that grompp now warns that "tau-p = 5 5"
> >>> isn't valid, but I think that's better than users thinking two values
> are
> >>> required for semiisotropic, or silently not getting what you might
> think
> >>> "tau-p = 5 10" might implement.
> >>>
> >>> I'll amend those docs to clarify this point.
> >>>
> >>> Mark
> >>>
> >>> On Fri, Feb 5, 2016 at 6:13 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >>>
> >>>>
> >>>>
> >>>> On 2/5/16 12:07 PM, Mark Abraham wrote:
> >>>>> Hi,
> >>>>>
> >>>>> Yes,
> >>>>>
> >>>>
> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
> >>>>> is
> >>>>> the fix for another bug that could in principle produce this
> behaviour,
> >>>> but
> >>>>> semiisotropic is supposed to take two real values, so something may
> be
> >>>>> amiss here.
> >>>>>
> >>>>
> >>>> tau-p should only read one value, unless I'm missing something in
> >>>> readir.c.
> >>>> Semiisotropic coupling requires two values of ref_p and
> compressibility,
> >>>> but
> >>>> tau-p is read as RTYPE, not STYPE.
> >>>>
> >>>> -Justin
> >>>>
> >>>>> Mark
> >>>>>
> >>>>> On Fri, Feb 5, 2016 at 5:41 PM Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >>>>>
> >>>>>>
> >>>>>>
> >>>>>> On 2/5/16 11:37 AM, Kortzak, Daniel wrote:
> >>>>>>> Dear All,
> >>>>>>>
> >>>>>>> when using gmx-5.1.2 with a mdp file with the following pressure
> >>>>>> coupling parameters:
> >>>>>>>
> >>>>>>> ; pressure coupling
> >>>>>>> Pcoupl = berendsen
> >>>>>>> Pcoupltype = semiisotropic
> >>>>>>> nstpcouple = -1
> >>>>>>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> >>>>>>> tau_p = 5 5
> >>>>>>> compressibility = 4.5e-5 4.5e-5
> >>>>>>> ref_p = 1.0 1.0
> >>>>>>> ; Scaling of reference coordinates, No, All or COM
> >>>>>>> refcoord_scaling = all
> >>>>>>>
> >>>>>>>
> >>>>>>> grompp gives the error message:
> >>>>>>>
> >>>>>>>
> >>>>>>> ERROR 1 [file parameter.mdp, line 387]:
> >>>>>>> Right hand side '5 5' for parameter 'tau_p' in parameter file is
> >>>> not a
> >>>>>>> real value
> >>>>>>>
> >>>>>>>
> >>>>>>> With versions below 5.1.2 everything seems to be fine. Are there
> >>>>>> additional changes beyond what is mentioned in the release notes or
> am
> >>>> I to
> >>>>>> blind to find the right section?
> >>>>>>>
> >>>>>>
> >>>>>> tau_p only takes one value (unlike tau_t, which needs one per
> >>>> thermostat
> >>>>>> group).
> >>>>>> The issue that was fixed was grompp silently ignoring extraneous
> >>>> input
> >>>>>> values,
> >>>>>> so previous versions carry on happily ignoring the stuff it doesn't
> >>>> need.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>
> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
> >>>>>>
> >>>>>> -Justin
> >>>>>>
> >>>>>> --
> >>>>>> ==================================================
> >>>>>>
> >>>>>> Justin A. Lemkul, Ph.D.
> >>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>>>>
> >>>>>> Department of Pharmaceutical Sciences
> >>>>>> School of Pharmacy
> >>>>>> Health Sciences Facility II, Room 629
> >>>>>> University of Maryland, Baltimore
> >>>>>> 20 Penn St.
> >>>>>> Baltimore, MD 21201
> >>>>>>
> >>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>>>>> http://mackerell.umaryland.edu/~jalemkul
> >>>>>>
> >>>>>> ==================================================
> >>>>>> --
> >>>>>> Gromacs Users mailing list
> >>>>>>
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> >>>>>>
> >>>>
> >>>> --
> >>>> ==================================================
> >>>>
> >>>> Justin A. Lemkul, Ph.D.
> >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>>
> >>>> Department of Pharmaceutical Sciences
> >>>> School of Pharmacy
> >>>> Health Sciences Facility II, Room 629
> >>>> University of Maryland, Baltimore
> >>>> 20 Penn St.
> >>>> Baltimore, MD 21201
> >>>>
> >>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>>> http://mackerell.umaryland.edu/~jalemkul
> >>>>
> >>>> ==================================================
> >>>> --
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> >>>
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