Extracting coordinates of solvents that are moving in a channel

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1

Hello Everyone,

I have completed an MD run and currently summarising the results. There are one polymer chain and ~ 35,000 methanol molecules as solvent.

I want to trim the number of solvent molecules and only have methanols that are close to the polymer walls (maybe using a cutoff). There are also some cavities (in the polymer) from where methanols are going inside and outside.

Can anyone suggest to me a way how to extract the methanols that moving near the polymer?

Thank you in advance.
Regards
Ranajit

2

Look at the nanotube permeation tutorial on VMD website.
Simulation of Water Permeation through Nanotubes (uiuc.edu)

The Tcl script described there could be of help. Obviously, it will need to be modified for your specific case.