[gmx-users] hbond error

[Justin Lemkul]

On 2/16/17 9:17 AM, Mark Abraham wrote:
> Hi,
>
> Great. To check that I understand you, do you think it should it read
> "Ordering is the reverse of that in -hbn index file?"
>

While this has been a point of confusion in the past, I think we have to be 
careful with the wording here.  The ordering of -hbn and -hbm *is* actually the 
same (the first element in -hbn is in fact the first matrix element in -hbm), 
but the user has to understand how to interpret the contents of an .xpm file. 
Its contents are printed as one sees it visually, so the first line of data is 
the top line of the matrix, but that's not the first element of the matrix.  So 
if we're going to clarify the language, we should probably have a rather more 
verbose explanation of how to map the entries, in terms of the .xpm content itself.

-Justin

> Mark
>
> On Thu, Feb 16, 2017 at 2:32 PM <chiara.parravicini at guest.unimi.it> wrote:
>
>> Hi,
>>
>> I just realized that the hbond tool works fine, but produces output in
>> reverse order. The "bug" is in the manual that states:
>>
>>   * -hbm:  existence matrix for all hydrogen bonds over all frames, this
>> also
>>     contains information on solvent insertion into hydrogen bonds.
>> Ordering is
>>     identical to that in -hbn index file.
>>
>> Chiara
>>
>> Il 16/02/17 13:41, *Mark Abraham * <mark.j.abraham at gmail.com> ha scritto:
>>> Hi,
>>>
>>> I'm not sure whether I properly understand your description of the
>>> behaviour. But if you think you have a case where the tool doesn't do
>> what
>>> its documentation says, please open an issue at
>>> https://redmine.gromacs.org
>>> and attach a tarball of files that will help us diagnose and fix it :-)
>>>
>>> Mark
>>>
>>> On Thu, 16 Feb 2017 13:01 Chiara Parravicini <
>>> chiara.parravicini at guest.unimi.it> wrote:
>>>
>>>> Dear Gmx users,
>>>>
>>>> using GROMACS version 2016.1, I found the following error in the
>>> output of
>>>> the gmx hbond routine: when computed from different groups, where
>>> one is a
>>>> subset of the other one, hbonds from the same acceptor/donor pair do
>> not
>>>> match.
>>>>
>>>> I known that this error has been already widely discussed in previous
>>>> gromacs versions. Is there any solution?
>>>>
>>>> Thanks
>>>>
>>>> Chiara
>>>>
>>>>
>>>>
>>>> --
>>>> Chiara Parravicini, PhD
>>>> Laboratorio di Biochimica e Biofisica Computazionale
>>>> Dipartimento di Scienze Farmacologiche e Biomolecolari
>>>> Università degli Studi di Milano
>>>> Via Balzaretti 9,
>>>> 20133 Milano, Italy
>>>> Tel: +39 02-503-18256/18355
>>>> Fax: +39 02-503-18284
>>>>
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
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>> --
>> Chiara Parravicini, PhD
>> Laboratorio di Biochimica e Biofisica Computazionale
>> Dipartimento di Scienze Farmacologiche e Biomolecolari
>> Università degli Studi di Milano
>> Via Balzaretti 9,
>> 20133 Milano, Italy
>> Tel: +39 02-503-18256/18355
>> Fax: +39 02-503-18284
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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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

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