"g_bond -d" reports long skewed bond that shouldn't be there
I'm using GROMACS version 3.1.4. When I use "g_bond -d" tool, it reports that one of the bonds is 13nm long in the first frame and gets longer and longer as the simulation progresses. By the last frame of the simulation, the bond is ~16nm long. Attached are the trajectory over 10 picoseconds of the simulation, the topology, and index for the protein, so you can run the tool and see the skewed bonds for yourself. The bond occurs at the 88th residue, between a carbon and hydrogen.
#3 Updated by David van der Spoel about 12 years ago
I think you have misinterpreted the manual. According to g_bond -h:
g_bond makes a distribution of bond lengths. If all is well a gaussian
distribution should be made when using a harmonic potential. bonds are read
from a single group in the index file in order i1-j1 i2-j2 thru in-jn.
This mean you can not simply give it the protein index file as it will interpret your list of atoms as bonds, some of them maybe quite far off.