metadynamics: colvars and hills prints

[Victor Volkov]

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

[Oliver]

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.

Oliver

[Victor Volkov]

Hello, Oliver.

Thank you for your point.

:-)

This helps.

Victor

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[Victor Volkov]

Dear Oliver:

I see this paper

https://wires.onlinelibrary.wiley.com/doi/abs/10.1002/wcms.90

devoted to the mass re-scaling parameter.

Best wishes.

Victor

On Mon, Dec 5, 2022 at 10:44 AM Oliver <olivie...@hotmail.com> wrote: