Date: Wed Aug 02 2017 - 20:00:22 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 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:
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 harmonic restraints?
Any help that could be offered would be much appreciated.
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:31 CST