[gmx-users] make_ndx treats "&" and "AND" differently -- expected?

Christopher Neale chris.neale at alum.utoronto.ca
Sat May 21 00:02:14 CEST 2016

Dear Users:

In an attempt to get around the '&' issue in index group names, I have tried using the 'AND' keyword, which is noted in the gmx make_ndx -h output. Indeed, the word "AND" replaces the ampersand in the index group in this case. However, the selection seems broken to me. Details are below. Specifically, with the '&' between selection of one atom name and one residue number, I get one atom in the group, as expected. However, when I use the 'AND' keyword, "r" seems to get promoted to "R" and then (for this or other reasons) the selection of one particular residue is not honored.

NOTE: same behaviour if using "AND" or "and"

Can anyone confirm whether this behaviour is indeed unexpected or whether I misinderstand the usage of "AND" ? I tried to look for info on make_ndx in the manual and the online documentation but there is no definition of what "AND" does, so I am presuming that it is intended to be the common interpretation.

$ echo -e "aC316 AND r1 \n aC316 & r1 \n q \n" | gmx make_ndx -f start.gro -o rdf.ndx
                 :-) GROMACS - gmx make_ndx, VERSION 5.1.2 (-:

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GROMACS:      gmx make_ndx, VERSION 5.1.2
Executable:   /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
Data prefix:  /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial
Command line:
  gmx make_ndx -f start.gro -o rdf.ndx

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   128      Other residues
There are:  6396      Water residues
There are:    34        Ion residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

  0 System              : 35862 atoms
  1 Other               : 16640 atoms
  2 DPPC                : 16640 atoms
  3 K                   :    17 atoms
  4 CL                  :    17 atoms
  5 Water               : 19188 atoms
  6 SOL                 : 19188 atoms
  7 non-Water           : 16674 atoms
  8 Ion                 :    34 atoms
  9 DPPC                : 16640 atoms
 10 K                   :    17 atoms
 11 CL                  :    17 atoms
 12 Water_and_ions      : 19222 atoms

 nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
 'a': atom        &   'del' nr         'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr        'splitat' nr    'h': help
 'r': residue         'res' nr         'chain' char
 "name": group        'case': case sensitive           'q': save and quit
 'ri': residue index

Found 128 atoms with names C316 AND R1

 13 C316_AND_R1         :   128 atoms

Found 128 atoms with name C316
Merged two groups with AND: 128 130 -> 1

 14 C316_&_r_1          :     1 atoms


Thank you,

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