Re: Unusual WT-Metadynamics gaussians heights

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Nov 13 2018 - 07:44:58 CST

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 how the 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>
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

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