[gmx-users] strange behaviout in 5.1.2

[Justin Lemkul]

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

==================================================