Re: how to use variables in colvar configuration file

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Sep 23 2011 - 13:23:55 CDT

Hi Emilia,

This has been discussed in the past on this mailing list, you can find
it in the archives (just googling usually works).

Depending on what you want to do to the force constant, the
time-dependent options might suit your needs. If you give more
details, I'll try and see if there is something simpler you can do.

Jerome

On 23 September 2011 19:26, Ling Wu <emilia.l.wu_at_gmail.com> wrote:
> Hi All,
> I am using colvar to restrain some part of my system, and I have a  colvar
> configuration file like this:
> -----------------------------------
> Colvarstrajfrequency 100
> Colvarsrestartfrequency 100
> colvar {
>    name head_POPC_up
>    distanceZ {
>       ref {
>          dummyAtom ( 0.000, 0.000, 0.000 )
>       }
>        main {
>              atomsFile head_POPC_up_main.ref   # head atoms #
>              atomsCol    B
>              atomsColValue      1.0
>          }
>    }
> }
> harmonic {
>   colvars head_POPC_up
>   centers 19 # or wherever the head group should be (15, 18, 17...) #
>   forceConstant 5
> }
> -----------------------------------------
> Is there any way I can define some variables for the forceConstant in the
> NAMD configuration file, so the parameter can pass to colvar configuration
> file  automatically? Thanks a lot!
>
> Emilia
>

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