Re: colvar: atom group defn. fails

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Apr 16 2010 - 07:17:38 CDT

Hi Neelanjana,

Can you please send me (off-list) a set of input files so that I can
try and reproduce this behavior?

Best,
Jerome

On 16 April 2010 12:29, Neelanjana Sengupta <senguptan_at_gmail.com> wrote:
> Hi NAMD experts,
>
> I am defining an rg colvar component as follows:
>
>         gyration {
>                 # atom group definition:
>                 atoms   {
>                                 atomsFile       s1.pdb
>                                 atomsCol        O
>                                 atomsColValue   2.0
>                 }
>         }
>
> However, NAMD fails to recognize this atom group definition, and complains:
>
> colvars:       Initializing atom group "atoms".
> colvars:       Error: no atoms defined for atom group "atoms".
>
> I could not figure out the problem here. I have used a similar module for a
> reference structure in RMSD (refPositionsFile, refPositionsCol,
> refPositionsColValue), and that had worked...
>
> Some pointers would be very helpful.
>
> Thanks,
> Neelanjana
>
>
>

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