End to end polymer distance calculation

[Tinto.Alencherry]

GROMACS version:
GROMACS modification: No
Here post your question

How to calculate end to end distance for a polymer system?
(I am not an expert in Gromacs and in the learning stage.)

I have a polymer (10 mer) and created a melt system with 50 individual chains. ~ 5500 atoms. I completed production run, and want to find the end-to-end distance (chain length) of an individual polymer chain. Could anyone help me with the procedure towards end-to-end distance calculation.
(Confused about the flow chart of procedure - do I need to generate index file, should I use gmx distance, gmx mindist or gmx pairdist?)

Thank you for your interest and response.

Kind Regards
Tnt

[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