Re: Shear flow simulation setup

From: Giacomo Fiorin (
Date: Wed Apr 26 2017 - 09:47:21 CDT

Hi James, the simple Google search "namd shear flow tutorial" should point
you to relevant commands. (You're welcome.)

That said, you should also try figuring out first how big the signal
(physical shear field) compared to the noise (lipid molecule protrusions,
membrane undulations and peristaltic fluctuations, etc).


On Wed, Apr 26, 2017 at 9:51 AM, James Starlight <>

> Hello,
> My case study is mechanosensation of the protein embedded into the
> membrane. I need to study the macromolecular conformational
> transitions altered under mechanical deformations which are caused by
> constant shear flow.
> I will be gratefull for any NAMD tutorial which explains technical
> details how to perform molecular simulations considering shear flow
> deformations (e.g locally or applied on the membrane as shear field),
> thus mimicking physiological conditions mediated by blood flow.
> Thanks for help!
> James

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

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