Re: How to setting tilt component in colvars module

From: 서용일 (seoyi86_at_gmail.com)
Date: Mon Sep 23 2013 - 22:54:26 CDT

Dear Fiorion

Thanks for your respond

This will be a help to me.

Best regards,
Yongil

2013/9/23 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>

> 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, 서용일 <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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