Re: Steered MD along detected routes

From: Munir S. Skaf (
Date: Sat Nov 16 2013 - 06:43:08 CST

Dear Johny,

Perhaps you don't need to define your SMD routes precisely along a cuved
path, but it may
turn out that a few (say, 3 or 4) turning points on a given pathway are
sufficient to smoothly
drive your ligand out of the enzyme.
You have to make educated guesses to define the turning points.
Please take a look at Leandro Martínez's work:

J. Phys. Chem. B 2008, 112, 10741–10751
  This multi-point SMD approach preserves the desired physics of the force

On Sat, Nov 16, 2013 at 9:10 AM, Johny Telecaster <
> wrote:

> Dear NAMD Developers,
> I have some questions about stereed MD. In particular I'd like to
> simulate ligand unbinding from the enzyme. Using CAVER Pymol plugin I've
> detected 3 possible paths inside my protein. Now I'd like to run stereed MD
> along each of that routes to measure forces affected on the ligand during
> its motions along each of it. How I could define force directions
> presicely along CAVER paths? Does it possible to define this pathes as the
> colvar restrictions? Please provide me with example.
> Many thanks for the suggestions,
> Johny T.
> Scanned and tagged with DSPAM 3.10.2 by Instituto de Quimica - Unicamp
> !DSPAM:106,5287537b107521489016123!

Munir S. Skaf
Institute of Chemistry - Cx. P. 6154
State University of Campinas - UNICAMP
Campinas - SP 13084-862, Brazil
Tel. 55 19 3521 3093 / Fax: 3521 3023

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