How to measure the water flux through an artificial channel in bilayer lipid membrane via GROMACS?

30 March 2017 1 316 Report

I am a beginner in using GROMACS, i am using MARTINI forcefield, and i created a bilayer lipid membrane (CG) and also a channel via insane.py (MARTINI forcfield tool), the issue is how to calculate the water flux through a defined channel, MARTINI forcefield founder they have offered a tool called fluxer.py, but the issue that there is no tutorial about how to use it.

Karolina Mitusińska

Is there any particular reason you want to use fluxer.py?

I could recommend you some other tools:

-flux that will graphically show you where water is flowing

-the newest tool of my research group, AQUA-DUCT, that will trace water molecules and also gave you some statistic data

-CAVER 3.0 taht will gave you some geometerical data of the tunnel

Best regards,

Karolina

Article Tracking the Flow of Water through Photosystem II Using Mole...

Article CAVER 3.0: A Tool for the Analysis of Transport Pathways in ...

Article AQUA-DUCT a ligands tracking tool

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