[gmx-users] strange behaviout in 5.1.2

[Erik Marklund]

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
>>>>>> 
>>>>>> ==================================================
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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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