csg_dump creates different results for LAMMPS and GROMACS

[Philipp Rosenauer]

Hello everyone,

I want to use VOTCA with LAMMPS to coarse-grain a polyimide. I started to work with VOTCA by following the tutorials and found that most tutorials are only for Gromacs so I also took a look at Gromacs and did the hexane tutorial. To learn everything for the big polymer I wanted to rebuild the Tutorial for LAMMPS but during the csg_stat I discovered some problems. The RDFs were quite different. 

So I went back and just did a simulation in LAMMPS and GROMACS with all forces set to zero. I also checked the coordinates for both LAMMPS (in an .xtc format) and the GROMACS .trj file and they were identical for all 1000 timesteps.

I also have the same --cg file: hexane.xml (only changed the names of the molecules accordingly to the output of csg_dump) 

I then proceeded with the following commands:
For LAMMPS:

csg_stat --top topo.xml --trj gromacs.xtc --cg hexane.xml --nt 24 --options settings.xml --begin 0

For Gromacs:

csg_stat --top topol.tpr --trj traj.trr --cg hexane.xml --nt 24 --options settings.xml --begin 0

So the hexane.xml files as well as the settings.xml files are identical.I assumed that the results should be the same but still the rdfs are different (see picture of nonbonded A-A below)

I attach the topo.xml file for the LAMMPS side and the settings.xml file as well and would appreciate every help I could get to understand where the mistake happens.

[Christoph Junghans]

My guess is that the tpr file has some exclusions in it and the xml
topology doesn't.
You can check that by using the topol.xml with the traj.trr or by
running csg_dump --top <file1> --excl and compare the output.
You can add exclusion to a topology by adding bonds, angle etc to the
mapping file.
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Christoph Junghans
Web: http://www.compphys.de