[gmx-users] strange behaviout in 5.1.2

[Mark Abraham]

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
> >>
> >> ==================================================
> >> --
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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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