Re: Unusual WT-Metadynamics gaussians heights

From: Bruno Cuevas Zuviría (bruno.czuviria_at_upm.es)
Date: Tue Nov 13 2018 - 10:16:51 CST

Oh it's right, the file I uploaded is not the right one, I have just
realised. Anyway, my output at initialization confirms that
well-tempered was on.

https://gist.github.com/BrunoCuevas/67dddc26c858f74701b67d230dcd0303

I compiled my namd from source code pushed the 2018-07-23 in Linux64
machine.

El 13/11/2018 a las 14:44, Giacomo Fiorin escribió:
> Hi Bruno, can you post the standard output at initialization time? 
> From the configuration file that you used, you do not have the
> wellTempered option on: therefore, I'm not sure howthe weight could
> change.
>
> If you are indeed observing Gaussians with variable height given your
> configuration, then please report also the code version you are using.
>
> Giacomo
>
> On Mon, Nov 12, 2018 at 5:27 AM Bruno Cuevas Zuviría
> <bruno.czuviria_at_upm.es <mailto:bruno.czuviria_at_upm.es>> wrote:
>
> Hi all
>
> I am working in a ligand-protein system using well tempered
> metadynamics. It was on my understanding that gaussians height should
> decrease according to the underlying free-energy landscape that is
> drawn
> by the gaussian deposition, so gaussians should never be larger
> than the
> maximum value that was set.
>
> However, I am reading from the hills file values higher
> (~0.3kcal/molA)
> than what I set (0.1kcal/molA). Why is this? Could it be related with
> the fact that my colvar has run out of the grid? Or with the fact
> that I
> am running a re-started colvars simulation?
>
> The colvars config file I am using is this one:
>
> https://gist.github.com/BrunoCuevas/3441584d7fc944bb1b97c2dbd90ce487
>
> Thanks in advance!
>
> --
> -------------------------------------------------------------------------
> Bruno Cuevas Zuviría
> Universidad Politécnica de Madrid
> Centro de Biotecnología y Genómica de Plantas - UPM/INIA
>
>
> ---
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>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin

-- 
-------------------------------------------------------------------------
Bruno Cuevas Zuviría
Universidad Politécnica de Madrid
Centro de Biotecnología y Genómica de Plantas - UPM/INIA
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