[gmx-users] Trouble with gmx distance

Justin Lemkul jalemkul at vt.edu
Fri Jul 11 01:04:03 CEST 2014

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 

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 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


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