colvar: atom group defn. fails

From: Neelanjana Sengupta (
Date: Fri Apr 16 2010 - 05:29:29 CDT

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.


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