[gmx-users] strange behaviout in 5.1.2

[Mark Abraham]

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
>> >>
>> >> ==================================================
>> >> --
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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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>> Gromacs Users mailing list
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>