Re: How to setting tilt component in colvars module

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Sep 23 2013 - 09:43:35 CDT

Hello Yi,

1. the lowest value and the highest value are 0 and 1, respectively.

2. x is the cosine indeed.

On Mon, Sep 23, 2013 at 2:21 AM, 꽌슜씪 <seoyi86_at_gmail.com> wrote:

> Dear NAMD users
>
> I want to get the tilted angle of protein.
> So, I using tilt component in colvars module.
> My colvars configuration file is below:
>
> colvar {
> name Rotation_protein
>
> width 1
>
> lowerboundary -1
> upperboundary 1
>
> tilt {
> atoms {
> psfSegID 8RA
> atomNameResidueRange CA 1-8
> }
> refPositionsFile ../colvars_orient/pdb file
> refPositionsCol B
> }
> }
>
> harmonic {
> colvars Rotation_ring
> forceConstant 1000.0
> centers 1.0
> targetcenters 0.0
> targetnumsteps 500000
> targetnumstages 90
> }
>
> I have some question.
>
> 1. I know the value of lowerboundary, upperboundary, centers and
> targetcenters are cosine(theta).
> but what is value of the width??
> I guess the value of width: the angle of degree? or radian? or other
> values?
> well, I put the degree, In my colvars configuration file.
>
> 2. The harmonic oscillator is k(x - x_0).
> But, I don't know x. x is theta? or cosine(theta)?
>
> Thanks for reading.
>
>

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