Re: Simulation of the mechanical stress in NAMD

From: Giacomo Fiorin (
Date: Mon Jul 17 2017 - 07:49:49 CDT

Yes to both, you can control the PBCs (to set e.g. the area strain) and
apply restraints or biasing potentials to the protein, but you need to
consider carefully the time scale of this process.


On Mon, Jul 17, 2017 at 3:55 AM, James Starlight <>

> Dear NAMD Users!
> I am using a molecular dynamics simulation for the investigation of
> the activation of Mechanic-sensing ionic channel. My question: is it
> possible to introduce a mechanical stress acting on the membrane or
> directly on selected part of the protein, assuming that its
> mechanic-sensing domains are known from the X-ray structure?
> Thanks for help!
> Gleb

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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