End to end polymer distance calculation

[alevilla]

HI,
you can generate an index file and the use gmx distance. This post may help you

Using gmx distance to calculate end-to-end distance between polymeric chains

GROMACS version: 2018.4 GROMACS modification: No Here post your question: I am trying to calculate the time averaged end-to-end distance of polymeric chains. I have 128 chains in my system and I want to compute an average end-to-end distance of these 128 chains as a function of time. I tried using an index file containing pairs of initial and final atom as follows: [Index] 1 10 11 20 21 30 … where 1, 10, … represent initial and final atom no of a single chain. I am not sure whether this…

In general for the difference between

@Tinto.Alencherry

gmx distance, gmx mindist or gmx pairdist

you can look to the following post

What is the difference between gmx distance, gmx mindist and gmx pairdist?

Hi, I am trying to compute distance between four residues of a protein involved in active site. I am getting confused in mindist, pairdist and gmx distance. What are the limits and differences in three? Which analysis can be helpful in plotting distance between A-B, B-C, C-D and D-A residues over time, where ABCD are 4 residues forming bottleneck for ligand entry.

Best regards
Alessandra