Calculating complexation ion interactions

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No

Hello dear community,

I have been studying the interaction between polymers with surfaces. Generally, this occurs mediated by an ion in a surface — ion — polymer form, where it is counted as interaction when the ion is interacting with the surface and the polymer simultaneously.

I use my own program to determine the amount of these interactions over time, but it is quite slow because the surface and polymers have several actives sites to interact.

I wonder if there is a way to do it with the Gromacs analysis programs to count these interactions. Unfortunately the gmx mindist program can only determine pair interactions I think.

Kind regards

2

Hi,
maybe gmx mindist together with option -on (number of contact) and -d (0.6) distance for contacts, and -ng (1) number of secondary groups to compute distance to a central group, can provide information that with a small analysis are in the direction

Or if you have already a code, maybe you can use analysis template (gromacs-202X.X/share/template/template.cpp) to build you on tools.
Here you can find some documentiation on Gromacs: Framework for trajectory analysis

Best regards
Alessandra

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