Re: colvar DistanceZ

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Nov 26 2014 - 07:25:03 CST

Thanks Jerome for your suggestion. I have read the documentation. So would
you like to explain how can we get the -65 from 40 and -55?

Regards,
Kevin

On 26 Nov, 2014, at 19:07, Jérôme Hénin <jerome.henin_at_ibpc.fr
<javascript:_e(%7B%7D,'cvml','jerome.henin_at_ibpc.fr');>> wrote:

Hi Kevin,

Please read the documentation for the distanceZ component.

Jerome

On 26 November 2014 at 04:03, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk
<javascript:_e(%7B%7D,'cvml','cchan2242-c_at_my.cityu.edu.hk');>> wrote:

> Dear Users,
>
> I am currently using DistanceZ for my colvars definition and everything
> goes fine except it does not gives me the value I expect.
>
> I thought DistanceZ was measuring the subtracted vector between the centre
> of mass of atoms in the main group and that in the ref group and then
> projected it onto the z-axis, in other words only the z component is of the
> interest. In my system,
> com of main locates at z=40
> com of ref locates at z=-55
> However the first step (step 0) of colvars.traj gives me -65 for DistanceZ.
>
> As I'm doing the umbrella sampling, it's fine if I change my windows list
> according to z=-65 but I'm just curious what DistanceZ was actually
> measuring.
>
> Thanks in advance,
> Kevin
> ukevi_at_gmx.hk
>
> Follow is the input parameters:
>
> colvar {
> name ProjectionZ
>
> width 0.25
>
> distanceZ {
>
> main {
> atomsFile main.pdb
> atomsCol B
> atomsColValue 1.0
> }
> ref {
> atomsFile ref.pdb
> atomsCol B
> atomsColValue 1.0
> }
> }
> }
>
> harmonic {
> colvars ProjectionZ
> centers 40
> forceConstant 4.0
> }
>
>

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