[CP2K:3124] Re: Metadynamics Bug report in colvar: DISTANCE

Teodoro Laino teodor... at gmail.com
Wed Mar 2 19:34:21 CET 2011


Dear Ata,

thanks for being so responsive, but I would like to make it clear that the DISTANCE cv (as is implemented in CP2K, with the name &DISTANCE) between
two atoms (i and j) is defined as :

sqrt( (xi-xj)**2 + (yi-yj)**2 + (zi-zj)**2)

that  IS equal to

sqrt ((-(xi-xj)*2 + (yi-yj)**2 + (zi-zj)**2)

There is no such reference x0,y0,z0 in the definition of a DISTANCE colvar. Where do you see it? Can you please cut&paste the whole subroutine, from begin to end of this colvar?
I'm just curious because the DISTANCE cv (as long as I remember) was never defined like that..

Teo

p.s.: I do not comment further the 200 number in your cutoff - I can give suggestion, but the choice is of the people doing their work.

On Mar 2, 2011, at 7:11 PM, Ata Roudgar wrote:

> 
> 
> Hi Teo,
> 
> 1. I am just talking about DISTANCE as collective variable and not
> ANGLE.
> 2. sqrt( (x-x0)**2 + (y-y0)**2 + (z-z0)**2) is NOT equal to sqrt ( (-x-
> x0)**2 + (y-y0)**2 + (z-z0)**2)
> 3. choosing inappropriate cutoff  energy resulting in a underestimate
> or overestimate the chemical bonds. It also introduces a huge pressure
> on the system called Pulay stress and therefore it strongly affects
> the result of NPT simulation and not NVT. It could affect on more
> result but definitely not a discontinuity of actual instantaneous
> collective variable after 18ps simulation. These two discussions are
> totally unrelated.
> 
> 5. It is possible that this bug affects on my simulation only since my
> metadynamics trajectory is very long, but for those people who might
> have the same problem as I had, they can fix this bug by just removing
> the line 2268 from the file colvar_methods.F:
> 
>    ss=ss-NINT(ss)
> 
> as I did so my simulation looks very good.
> 
> Cheers,
> Ata
> 
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