[CP2K-user] [CP2K:18185] Re: metadynamics: colvars and hills prints

[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 <olivier_bouty at hotmail.com> wrote:

> 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
>
> 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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