From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Aug 02 2013 - 10:29:12 CDT
Hi Christopher,
I don't have everything in mind right here and now, but I suggest you give a CVS build a try. NAMD 2.9 is getting a little old, and we did some refactoring work on these things since then, to make them more general and consistent. Before that, the somewhat non-standard colvar definition that you are implementing had not crossed our mind, so it hadn't been tested.
Cheers,
Jerome
----- Original Message -----
> NAMD users,
>
>
> I'm trying to make use of the RMSD collective variable via the
> colvars module, but I seem to be having a syntax problem.
>
>
> I would like to align the system using atomNumbers 1276 1277 1278
> 1279, but compute the RMSD for atomNumbers 1 2 3 6 8 10 12 13 (all
> atom numbers are given as 1-based indices). Based on the
> documentation and experimentation, I have settled on the following
> as my best guess at the correct syntax:
>
>
>
> colvar {
> name m_rmsd
> rmsd {
>
>
> atoms {
> atomNumbers 1 2 3 6 8 10 12 13
> centerReference yes
> rotateReference yes
> refPositionsGroup {atomNumbers 1276 1277 1278 1279}
> refPositionsFile sys.pdb
> }
>
>
> refPositionsFile rmsd.ref
> refPositionsCol B
> refPositionsColValue 1.0
> }
>
>
> }
>
>
> in which,
> sys.pdb is the PDB file for all atoms in the system with the initial
> coordinates
> rmsd.ref is the PDB file for all atoms in the system with the initial
> coordinates, but the beta column for atoms 1 2 3 6 8 10 12 13 are
> set to 1.0 (all else are 0.0)
>
>
> The simulation runs without error, however, yields RMSD output
> indicating that it is BOTH aligning by and computing rmsd for atoms
> 1 2 3 6 8 10 12 13. I'm running NAMD 2.9 (the April 30, 2012 binary)
> on MacOSX 10.7.5.
>
>
> Thanks in advance for you help and suggestions!
> Christopher Mayne
>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:32 CST