From: Hossein Mohammadiarani (hm2006_at_wildcats.unh.edu)
Date: Mon Aug 24 2015 - 12:53:14 CDT
Dear NAMD users/developers,
I am working on a metadynamics simulation to understand peptide folding in two collective variables. I notice that NAMD generates a colvars.state file which contains a lot of numbers and Hill information. I have two main questions about the colvars.state file:
1] After some brief information on CVs in the header, numbers appear in the three column format followed by zeros then followed by some finite values periodically. I am not sure what each of these numbers represents. I could not find information on the format of this file although users guide has a brief description about it in the output files.
2] Toward the end in colvars.state file, hill data is expressed like below:
hill {
step 26215000
weight 1.00000000000000e-01
centers 1.42013145758478e+01
widths 2.00000000000000e-01
}
The question is why the step begins from somewhere in the middle of the simulation but not from the start of simulation.
I would be grateful if someone can help clarify these doubts.
Thank you
Hossein
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