[CPMD-list] PBC in MetaDynamics

[Nisanth Nair]

Dear Ali,

For distance (DIST) CV, the distance is NOT calculated with PBC, irrespective 
of the SYMMETRY.

For all coordination number types of CVs, the individual distances in rational 
functions/fermi functions are calculated WITH  PBC.

For dihedral angle, the PBC, is bit different. The collective coordinates are 
within -Pi and +Pi, while collective variables are within 0 and 2Pi.

If you want to introduce the PBC for DIST, you have to implement it for the 
collective variables and collective coordinates. So, it is bit involved, and 
difficult to explain in single email. The best will be you start tyring out 
yourself, and ask doubts if you have any. You have to start looking at the 
routines meta_colvar_inp.F, especially the part  SUBROUTINE COLVAROFR.
Look at some of the routines in meta_cv.F how PBC is incorporated while 
calculating distances. In meta_exlagr.F, and meta_hpot.F for implementing PBC 
for distances for collective coordinates and their displacements.

Now, if you use distance between atoms which are not bonded, in metadynamics, 
you will be sampling almost all possible distances before you get them 
bonded; meaning you may have to wait for ages, unless you are lucky or they 
are some radicals.
To sample only the relevant part of the free energy surface, i.e. to restrict 
the system to sample only specific range of distance, use keywords WALL+ 
and/or WALL- . Wrap you coordinates before you start, and keep the distances 
within say 4 or 5 Angstrom.

Best of luck.
Nisanth


On Wednesday 21 November 2007 19:40, Ali Hassanali wrote:
> Dear CPMD users,
>
> I haven't had any response on this issue so I'll try again. Does anyone
> know how CPMD handles PBC conditions in metadynamics? So lets say you had
> a collective variable being the distance between two atoms and the two
> atoms sampled the distance moving away from each other. Within normal PBC,
> the bond (distance between the atoms) will close in again.
>
> Or does metadynamics not deal with PBC in its implementation?
>
> Ali
>
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 Nisanth N. Nair
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 Email: nisanth.nair at theochem.ruhr-uni-bochum.de
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