[gmx-users] Measuring bond distances, angles and dihedrals

[Robert Cordina]

Hi,

I've carried out a number of equilibrations and I now want to extract bond distances, bond angles and dihedrals from the resulting trajectories.  I'm using MDTraj to do this, which is working perfectly fine, however I'm not too happy with the results as they are not exactly how I want them.  I am using modelling quite small molecules, so I'm only measuring distances, angles and dihedrals a few atoms apart.  I'm doing this to start parameterising a new coarse-grained force field, and for example I get a bond angle of 160 degrees, when really it should be 180 degrees.  This is happening because I'm calculating the angle between specific atoms spaced only 3-4 atoms apart which might be on opposite sides of a straight chain of carbon atoms.  What I'd like to get out is the angle between the centroid of the groups of atoms that would form the coarse-grained beads.

Does anyone have any suggestions if this can be done in GROMACS, or in any Python library which works with GROMACS?

Thanks,

Robert