[CP2K:3117] Metadynamics Bug report in colvar: DISTANCE

Teodoro Laino teodor... at gmail.com
Wed Mar 2 06:44:05 CET 2011


Dear Ata,

thanks for reporting this possible issue. Unfortunately I do not think it is something inappropriate in the definition of the CV rather an inappropriate usage of the CV.
In fact, as long as you do periodic simulations (i.e. condensed phase system) it would be totally wrong to switch off the PBC call, because by definition your atoms are at a distance defined by the PBC.

Instead if you want to do an isolated system, then very probably you did not specify PERIODIC NONE in the cell section.

In both cases, it could be something wrong (specified by you) in the parity of the coordination CV), which should be invariant for r-> -r : more is hard to say since you did not provide any input file.

Moreover there is no such keyword for ANGLE colvar: the only CVs which have implemented a PBC key is the DISTANCE_FUNCTION, XYZ_DIAG, XYZ_OUTERDIAG.

Double check your stuff and in case come back with an input file: maybe the situation will be less confusing.
Regards
Teo

On Mar 2, 2011, at 1:47 AM, Ata Roudgar wrote:

> Hi,
> I have so much fun with CP2K and really appreciate everyone who
> contributes to this software. I am performing metadynamics on a system
> of Triflic acids and the purpose of this metadynamics is to calculate
> the activation energy or so called reconstruction free energy of
> lateral proton transfer. The proton which is in form of hydronium
> should overcome a hydrogen bond and travel along y direction (around
> 7bohr) and reach to  transition state and then provide a final state.
> 
> There is a inconsistency which introduce a bug to my metadynmics:
> File   colvar_methods.F
> 
> line 2265 - 2269
> 
>    CALL get_coordinates(colvar, i, xpi, my_particles)
>    CALL get_coordinates(colvar, j, xpj, my_particles)
>    ss=MATMUL(cell%h_inv,xpi-xpj)
>    ss=ss-NINT(ss)
>    xij=MATMUL(cell%hmat,ss)
> 
> For my system  line 2272: ss=ss-NINT(ss) is totally inappropriate.
> Here is the explanation about what these lines do.
> 
> The first two lines get the coordination of two atoms which are listed
> in DISTANCE colvar. ss in third line calculate the coordination
> difference between these two atoms in direct coordinate (not in
> Cartesian). The forth line consider periodic boundary condition which
> means if the distance between two atoms during the metadynamics become
> more than half of the unitcell, this line will consider the atoms of
> the next unitcell to calculate the distance. Thus there will be huge
> jump in my real CV (S(r)) from x to -x or from y to -y or z to -z.
> This brings a huge difference between k(s-S(x)) and consequently a
> huge jump in total energy. So, it might a be good idea to implement a
> keyword (like the one in angle) to tell the user if he need a periodic
> boundary condition or not during metadynamics. I hope it help to
> improve the next version of CP2K
> 
> Regards,
> Ata
> 
> 
> 
> 
> 
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