From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Aug 24 2015 - 13:04:50 CDT
Dear Hossein,
The first list of data is the biasing potential (the sum of the hills)
discretized on a grid. Then the list of individual hills only includes
those hills that extend beyond the grid boundaries, and hence cannot be
properly described by the grid.
Best,
Jerome
On 24 August 2015 at 19:53, Hossein Mohammadiarani <hm2006_at_wildcats.unh.edu>
wrote:
>
> 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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