End-to-end distance of the protein

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
1.I want to calculate end to end distance of a proteins 1 atom and last atom how should i do that?
2.I’m only getting 8 frame for distance measure.what could be the potential cause?

2

You can either use gmx distance or gmx pairdist to calculate the distances. One calculates the pairwise distances within a selection group, the other calculates pairwise distances from one reference selection group to one, or more, other groups. If you make an index.ndx file with the first and the last atom of the protein in one selection group you can use gmx distance to calculate the distance.

If you only get 8 frames in the distance measurement output, you probably only have 8 frames in your trajectory.