From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Aug 27 2015 - 04:27:00 CDT
Dear Hossein,
For your next runs, if you want a detailed history, you probably want to
enable the option "writeHillsTrajectory".
You can still reconstruct it based on the colvars trajectory file
(*.colvars.traj), if you have one. That is, provided you're not running
well-tempered metadynamics, which would involve more work figuring out the
variable hill height.
Best,
Jerome
On 27 August 2015 at 01:05, Hossein Mohammadiarani <hm2006_at_wildcats.unh.edu>
wrote:
>
> 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 Jérôme Hénin <
> 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> 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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