Colvars RMSD syntax with a moving reference frame

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Fri Aug 02 2013 - 10:14:47 CDT

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

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