Hi Balaji,
I know that Helmut Grubmuller et al have been doing 'computational electrophysiology' with a modified version of gromacs, however currently there is no similar routine available in amber.
What you could try with amber is the double bilayer approach, where you set up two membranes with an ion imbalance on either side creating an ion gradient and thus transmembrane potential, see papers from Andrey Gurtovenko. However the potential will only exist until either the ions move through your membrane protein or through the membrane itself to equilibrate the imbalance (if the potential is too high the ions may actually cause a rupture of the membrane creating a water pore).
Cheers,
Callum
________________________________________
From: Balaji Selvam <bselvam01.gmail.com>
Sent: Thursday, February 18, 2016 8:22 PM
To: amber.ambermd.org
Subject: [AMBER] membrane potential
Dear AMBER users,
I am wondering is there a way to include membrane potential in AMBER14. I
am performing membrane protein simulation and looking for this option to
include in amber. I could not find any documentation regarding this.
I came across the post "
http://archive.ambermd.org/201212/0410.html" in
forum but no reply to this post.
Kindly advice.
Many Thanks,
Balaji
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Received on Fri Feb 19 2016 - 10:30:02 PST
