Metadynamics Bug report in colvar: DISTANCE

Ata Roudgar rou... at yahoo.com
Wed Mar 2 19:11:07 CET 2011



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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