Re: Steered MD simulation with pull and rotation

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Mar 29 2018 - 06:37:55 CDT

Hello Dhiraj, it sounds like you could achieve this with a combination of
the distanceZ and spinAngle collective variables:
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_distanceZ
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_spinAngle

with a moving harmonic restraint acting on both.

Giacomo

On Wed, Mar 28, 2018 at 3:23 PM, Dhiraj Srivastava <dhirajks_at_gmail.com>
wrote:

> Hi all
> I want to do simulation of my protein where I want to pull out a
> helix and rotate it simultaneously. is it possible to do it in NAMD or I
> have to do one at a time? also, is there any tutorial or example for such
> kind of simulation, specially both at the same time or rotation?
>
> Thank you
> Dhiraj
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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