[CP2K-user] [CP2K:18145] Re: metadynamics: colvars and hills prints

Oliver olivier_bouty at hotmail.com
Mon Dec 5 07:44:27 UTC 2022

Hi Victor,
Regarding your first question, i suggest reading the tutorial by M Ianuzzi: 
Simple metadynamics simulation using the coordination numbers as variables.
At the end of "second task", it can be read: instantaneous values of the 
CVs, instantaneous gradient of the bias potential with respect to the CVs, 
gradients of wall potentials with respect to the CVs, instantaneous value 
of bias potential, instantaneous values of wall potentials.
Hope it helps.

On Friday, 2 December 2022 at 09:16:36 UTC+1 volk... at gmail.com wrote:

> Dear developers and users:
> good evening-morning.
> I attach Meta files to drive for tetracycline side-group rotation,
> while it is under intra-molecular hydrogen bonding.
> For convenience, I attach the input, hills, colvars and current xyz files.
> Apparently, at present, the system made over the barrier in one direction
> but it is not yet "hot enough" along the colvar to swing back.
> *Question 1:*
> For 1 collective variable, the COLVAR file reports 11 columns.
> The 1st is time, the  6th and 10th are "dummy zeros", and the 11th is 
> temperature, 
> I assume the 2nd is CV.
> The manual does not specify what are the other six columns:
> I read in a previous discussion that they should account 
>  MTD_Force,   WallPot_F,   MTDPot,  WallPot and something else.
> Would you help to bring certainty?
>  *Question 2:* 
> Since Galileo got blind in his life-detention, there is a practice in 
> physics to pay attention to mass.
> How does CP2K require MASS  in  &METAVAR to be determined 
> for different types of possible constrained activities,
> or it is a formal scaling factor to keep in a certain range?
> *Question 3:*
> Exploring meta presentations on results, I noticed some developers
> use time/hills degree of freedom in respect to which they print properties.
> If I did not misinterpret, apparently, researchers normalize time by the 
> number of gaussians invested to flex along a collective variable. 
> How to print the number of hills to explore meaning of such approach?
> *Thank you!*
> Nice weekend.
> *Do not make it too good or you might end as Galileo. *
> Victor

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