[gmx-users] Trouble with gmx distance

[Justin Lemkul]

On 7/10/14, 11:55 PM, Teemu Murtola wrote:
> The help text explains this: "Each selection specifies an independent set
> of distances to calculate. Each selection should consist of pairs of
> positions, and the distances are computed between positions 1-2, 3-4, etc.
>
> In other words, the selections resemble those that were earlier required by
> g_bond, not those by g_dist. The wiki page on tool changes for 5.0 shows an
> example if using "plus" in a selection to get the behavior of g_dist to
> compute the distance between centers-of-mass of two groups.

Thanks, Teemu.  I guess this just comes down to perhaps a need for a bit of 
better wording in the documentation.  I guess I didn't recall that there was an 
example on that page.

-Justin

> On Jul 11, 2014 2:04 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>> Hi All,
>>
>> I have encountered a very annoying problem with gmx distance (the 5.0
>> replacement for g_dist/g_bond) - selections must have an even number of
>> atoms. Can anyone explain why this is necessary?  I designed a minimal test
>> system (distance between two atoms), and got:
>>
>> -------------------------------------------------------
>> Program:     gmx distance, VERSION 5.0
>> Source file: src/gromacs/trajectoryanalysis/modules/distance.cpp (line
>> 198)
>> Function:    void gmx::analysismodules::{anonymous}::checkSelections(const
>> SelectionList&)
>>
>> Inconsistency in user input:
>> Selection 'first' does not evaluate into an even number of positions (there
>> are 1 positions)
>>
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> Indeed, the code makes sure the selection size is a multiple of 2, but
>> why?  Is there a workaround?  Not all groups are even :)
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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