Re: Shear flow simulation setup

From: James Starlight (
Date: Thu Apr 27 2017 - 07:09:25 CDT

Hi Giacomo and thank you for the suggestions!

I have already seen that tutorial of the modeling shear flow using
built-in TCL script which is provided along with NAMD input file.

IMHO this aproach was very general sollution which would be tricky
adapt for my case-study - shear flow applied on the membrane or
selectively on the embedded protein. In principle it would be
interesting for me to test both aproaches if someone had already
approved it for the membrane systems.

BTW would it be reasonable in my case-study to make simulation with
the introduction of membrane tension of various magnitude , e.g which
has been approved there:

I thanks everyone for the additional suggestions!


2017-04-26 18:47 GMT+04:00 Giacomo Fiorin <>:
> 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).
> Giacomo
> On Wed, Apr 26, 2017 at 9:51 AM, James Starlight <>
> wrote:
>> 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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:15 CST