From: philippe Bourly (philippe.bourly20_at_gmail.com)
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:
But the simulation is running when the boundaries are set as:
Here is the harmonic restraint declaration:
Does anybody can explain me the link between the boundaries and the
Any help that could be offered would be much appreciated.
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