Q=9B=9E=E5=A4=8D:__Free_energy_(eABF):_ne?= gative RMSD and harmonic restraints.

Hello!

 

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                  r_RMSD

700       1.03274270310920e+02   1.01591786e+02 1.3150133e+00   -5.99159093081978e-01 

 

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.

 

Philippe