[gmx-users] water permeations study in channel using Gromacs

Nikhil Maroli scinikhil at gmail.com
Sat Mar 26 13:19:31 CET 2016

Dear all,

i have made cyclic peptide nanotube using charmm36 ff and done a 100ns MD.
now i wanted to study the water permeation inside the channel is there any
method available in Gromacs? i tried pulling the water from top of the tube
to bottom (channel is embedded in lipids) using US methods but it was not

Is there any way i can know the permeation details such as conductivity
,water distribution inside the channel etc..

PS : i seen many paper ,most of them used NAMD for these studies.

Nikhil Maroli

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