[gmx-developers] AnalysisNeighborhoodSearch and Selections

David van der Spoel spoel at xray.bmc.uu.se
Sun Jul 23 20:14:47 CEST 2017

Not sure what I'm doing wrong. My selection consists of the OW atoms in 
water molecules, then I'm trying to use the following code:

// Use neighborsearching tools!
AnalysisNeighborhoodSearch     nbsearch = nb_.initSearch(pbc, sel);
AnalysisNeighborhoodPair       pair;
AnalysisNeighborhoodPositions  positions(fr.x, fr.natoms);
AnalysisNeighborhoodPairSearch pairSearch =

while (pairSearch.findNextPair(&pair))
    int pi = pair.refIndex();
    int pj = pair.testIndex();

    printf("pi %d pj %d\n", pi, pj)


pi 0 pj 1
pi 0 pj 2

Note that "sel" just holds 0, 3, 6, 9, but the pairSearch algorithms 
gives atoms that are outside the selection. What is wrong?

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

More information about the gromacs.org_gmx-developers mailing list