Re: Format of colvars.state

From: Hossein Mohammadiarani (hm2006_at_wildcats.unh.edu)
Date: Wed Aug 26 2015 - 18:05:19 CDT

Dear Jerome:
Thanks very much for your quick response. I am relatively new to colvars module and have some more queries about the colvars.state file, etc.:

1. For the data described on the grid, is it possible to recover hill information similar to as reported for those hills that extend beyond the grid boundaries. For example, starting at step zero if one wants information in the following format:
hill {
      step 0
      weight
      centers
       widths
      }

2. If one wants to regenerate PMF as a function of time from a metadynamics run that only saved the final PMF, is it possible to do? If so, how to proceed for recovering that information? In my most recent runs, I learned that I can write PMF files frequently, but I have some previous metadynamics data for which I did not save PMFs and would like to recover that data, if possible.

Best,
Hossein

________________________________
From: heninj_at_gmail.com <heninj_at_gmail.com> on behalf of Jrme Hnin <jerome.henin_at_ibpc.fr>
Sent: Monday, August 24, 2015 2:04 PM
To: Namd Mailing List; Hossein Mohammadiarani
Subject: Re: namd-l: Format of colvars.state

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<mailto: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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