Free energy (eABF): negative RMSD and harmonic restraints.

From: philippe Bourly (
Date: Wed Aug 02 2017 - 11:45:56 CDT


I am a newbie in free energy. I am trying the protein/ligand free energy
tutorial of NAMD and I have some questions.

1. I am testing a part of the tutorial where the collective variable is an
angle and the RMSD of the ligand is restrained. When I checked the traj
file, I saw some negative values for the RMSD:

# step Theta r_Theta RMSD

700 1.03274270310920e+02 1.01591786e+02 1.3150133e+00

Does anybody know why? And do you think that will impact my calculation,
since my collective variable is the angle (Theta) and not the RMSD?

2. Finally, I have a question about the harmonic restraints. For one of the
harmonic restraints, my simulation crashed (ERROR: Constraint failure in
RATTLE algorithm) when I set the boundaries as:

lowerBoundary -180

upperBoundary 180

But the simulation is running when the boundaries are set as:

lowerBoundary 0

upperBoundary 360

Here is the harmonic restraint declaration:

harmonic {

   colvars Phi

   forceConstant 0.1

   centers -7.0


Does anybody can explain me the link between the boundaries and the
harmonic restraints?

Any help that could be offered would be much appreciated.


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