Re: Colvars Configuration File

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Wed Aug 19 2009 - 05:03:34 CDT

Hi Giacomo and others,

The CVS version of the user's guide containing colvars was more informative.
Based on it, this is how the *component par*t of my colvars config file
looks like, for a single dihedral component:

        dihedral {
                myatoms {
                        group1 { 1 }
                        group2 { 2 }
                        group3 { 3 }
                        group4 { 4 }
                        atomsFile component.pdb
                        atomsCol O
                        atomsColValue 4.00
                        psfSegID TRAN
                }
        }

However, I am getting this error message at runtime:

colvars: Initializing a new collective variable.
colvars: # name = omgprm
colvars: Initializing a new "dihedral" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Error: definition for atom group "group1" not found.

Can I please get some help and some pointers with this?

Thanks a lot.
Regards,
Neela

On Mon, Aug 17, 2009 at 7:16 PM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>wrote:

> Hi Neela, I didn't feel necessary to repeat the instructions on how to
> download the CVS (i.e. development) version of NAMD, because the
> relevant webpage is linked directly from the NAMD main webpage ("Build
> from Source Code").
>
> I paste its address here again for your convenience.
>
> http://www.ks.uiuc.edu/Research/namd/development.html
>
> Giacomo
>
> ---- ----
> Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science
> Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> work phone: (+1)-215-204-4216
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_<at>_gmail.com
> ---- ----
>
>
>
>
>

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