[gmx-users] strange behaviout in 5.1.2

[Erik Marklund]

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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