Re: reconstructing pmf

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Dec 18 2017 - 19:40:03 CST

If you do have the state file saved, the next run after loading it should
print the PMF file again.

Giacomo

On Dec 18, 2017 7:38 PM, "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov> wrote:

> Hi Stefano,
>
> I haven't done it myself, but wouldn't you just need to write a script to
> re-add the hills that metadynamics is adding yourself, based either on the
> colvars.traj file (ideally) or worst case recalculating your reaction
> coordinate trajectory from the dcd? The end result should in principle be
> the same if you saved these values at the same frequency that hills are
> added, albeit with a large chance of making a mistake somewhere in code if
> you don't have a working example to make sure that your script does what it
> is supposed to.
>
> -Josh
>
> On 12/18/2017 05:29 PM, Stefano Guglielmo wrote:
> Dear NAMD users,
> is it possible to reconstruct pmf of a metadynamics simulation (if for
> some reason the original file was corrupted or lost) in the same format as
> the one written as output by NAMD?
> Thanks in advance
> Stefano
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
>
>
>
>

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