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

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1

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 is giving me the desired output. Please suggest any better way to do this.

Thanks & Regards,
Mangesh

2

Hi,
now you can run gmx distance using the index file as input together with xtc and tpr file and the option -oav for output.
you will get the time serie of average distances (see gmx distance — GROMACS 2021.1 documentation)
Best regards
Alessandra

3

Hi Alevilla,

Thanks for your response.

I had done same thing while running “gmx distance” command. The main concern i had was whether the index file will be read as N/2 pairs as written in the “index.ndx” or else it will read all the atom numbers and give an average of N-1 pairs(assuming N atoms were mentioned in that specific index). I verified this by giving different number of pairs in my index and then checked the “-oall” output file for no. of distances. The index file is working properly and giving me the desired output.

Thanks again!

Regards,
Mangesh

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