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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.