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

From: yjcoshc_at_gmail.com
Date: Wed Aug 02 2017 - 20:00:22 CDT

1. It seems you are using eABF on the theta and RMSD. The r_RMSD is the value of extended variable, not the real RMSD.
2. The center of harmonic restraint usually keeps the same as the boundaries. It's strange that you set it to -7.0 while the theta ranges from -180 to 180.

-------- 原始邮件 --------
主题:namd-l: Free energy (eABF): negative RMSD and harmonic restraints.
发件人:philippe Bourly



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.



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