Ion swapping in computational electrophysiology

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No
Dear users,

I am performing an Ion/water position swapping with computational electrophysiology. I already have 100ns simulated and I want to make an analysis to check the ion/channel residues interactions. I need to apply this analysis for a duplicate system. So, I was wondering if gromacs presents a way to perform this analysis.

Thank you in advanced for your help

Anna

2

Hi Anna,

maybe the following documentation can help you.
GROMACS manual:

mdp option

Best regards
Alessandra

3

Hi Alessandra,

Thank you for your answer. I have already checked these two link. Neither of them contains the information I am looking for.

I am interested in the analysis of non-bonded interactions between ions crossing the channel and channel residues. You know how I could do?

Thank you in advanced for your help

Anna

4

Hi,
you can monitor and identify the contact between ion/ions and residues in the channel using gmx mindist, or you can use gmx pairdist to monitor vs time a specific distance between two groups.
Best regards
Alessandra

5

Hi alessandra,

I will try.

Thank you very much.

Best,
Anna