# Re: use Colvars to track four group of pair atoms distance at same time?

From: yjcoshc_at_gmail.com
Date: Fri Nov 22 2019 - 20:42:11 CST

Hi Jiali,

You need to specify the centers for CV length2 and length3 also.
According to
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic
, the centers keyword accepts a space-separated list of colvar values.
That means you may need to modify "centers 4.8" to something like
"centers 4.8 1.2 3.4", and the number 1.2 and 3.4 are the centers of
harmonic restraints for length2 and length3 respectively.

Best regards,

Haochuan Chen

> Dear Haochuan,
> Thank you so much for your help!! Does it means the harmonic constant
> part, i also need to make three parts? I found if I list three pair
> length together, it's not working?
> harmonic {
>   name lenpot1
>   colvars length1 length2 length3
>   forceConstant 1         # in kcal/mol/A^2
>   centers 4.8             # go from 25 Angstrom RMSD...
>   outputCenters on
> }
>
> Thank you so much for your help!
> jiali
>
> On Fri, Nov 22, 2019 at 2:23 PM <yjcoshc_at_gmail.com
> <mailto:yjcoshc_at_gmail.com>> wrote:
>
> Hi Jiali,
>
> You may need four independent colvar sections. For example:
>
> colvar {
>
>      name dist1
>
>      distance {
>
>          ...
>
>      }
>
> }
>
> colvar {
>
>      name dist2
>
>      distance {
>
>          ...
>
>      }
>
> }
>
> Best regards,
>
> Haochuan Chen
>
>
> 在 2019/11/22 下午12:59, Jiali Wang 写道:
> > Dear NAMD users,
> > Good afternoon, Is that possible to tracking four pair atom
> distances
> > independently at same time and apply harmonic constant? I am
> trying to
> > use four  part of distance { }. But I found in the colvars.traj
> file,
> > it only provides one column distance tracking results. Could
> some help
> > me with this?
> > Thank you for your time!
> > Jiali
> >
> > colvar {
> >   name length
> >   outputAppliedForce off
> >
> >   distance {
> >     group1 {
> >       atomNumbers 11530
> >     }
> >     group2 {
> >       atomNumbers 10888
> >     }
> >     }
> >   distance {
> >   group1 {
> >       atomNumbers 5266
> >     }
> >     group2 {
> >       atomNumbers 4624
> >     }
> >     }
> >   distance {
> >   group1 {
> >       atomNumbers 11794
> >     }
> >     group2 {
> >       atomNumbers 17152
> >     }
> >   }
> > }
>

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