csg_map - all molecules share the same name in frames extracted from .trr or .xtc with --no-map option

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Apparently, csg_map only recognizes one molecule name, even when used without a 
mapping file, i.e. --no-map option.

What steps will reproduce the problem?

1. If one takes a system with solute and solvent, and extracts frame(s) from 
the original Gromacs trajectory (.trr) using csg_map, then everything will be 
correct except for the fact that the same name will be assigned to all species, 
both solute and solvent - the first found molecule name.

What is the expected output? What do you see instead?

- Molecule names must be preserved in the extracted frames (.gro, .trr etc).

Low priority because Gromacs tool trjconv can be used for the same purpose. 
Still, csg_map should do the job correctly.

Original issue reported on code.google.com by abruk...@googlemail.com on 10 Oct 2014 at 11:50

[GoogleCodeExporter]

I did:
$ csg_map --top atomistic_files/topol.tpr --out dppc.gro --cg 
"dppc.xml;water.xml" --trj atomistic_files/dppc128_after_40ns.gro
with data from:
<https://code.google.com/p/plumx/source/browse/#git%2Fdppc_mapping>
and the molecule names are correct.

So please, check your mapping files again or upload them here.

Original comment by christop...@gmail.com on 10 Oct 2014 at 10:12

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You missed that I did NOT use any mapping files, but the option --no-map

Original comment by abruk...@googlemail.com on 10 Oct 2014 at 10:18

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I was able to reproduce this issue using:
$ csg_map --top atomistic_files/topol.tpr --out dppc.gro  --trj 
atomistic_files/dppc128_after_40ns.gro --nframes 1 --no-map

gro and pdb writer are affected, however csg_dump isn't.

I guess the issue is that the residue nr (and residue name) is relative to the 
molecules' resnr and not global.

Original comment by christop...@gmail.com on 11 Oct 2014 at 10:06

• Changed state: Accepted

[GoogleCodeExporter]

This issue was closed by revision 31e7084bbaf5.

Original comment by christop...@gmail.com on 12 Oct 2014 at 3:34

• Changed state: Fixed