Re: metadynamics simulations slow down and down

From: OiniL (
Date: Mon Oct 11 2010 - 09:36:29 CDT

Giacomo and Jerome:
Thank you very much for your reply!
The 'useGrids' option was set as default, so it was turned on.
It turns out that the 'expandBoundaries' option affects the computing
efficiency, especially when the colvars reach the boundaries.
This problem was solved by setting 'expandBoundaries' on.

However, this makes something seeming wrong when the simulation goes upto 100
Everything was normal during the first 100ns, but the colvars then began to be
 trapped at the values near the boundaries.
ex. : settings for colvar1:
{ upperBoundary 27
   upperWall 26.5}
and the value of colvar1 was about 26.5<=colvar1<=27.
It seems like there is some energy well at the boundaries during the
simulation but there is no any in fact.

some more configs:
{ upperBoundary 27.0
    expandBoundaries on
    upperWall 26.5

    upperWallConstant 500.0

What made this problem?
Any help or hint is appreciated
Best regards!

Cheng TAN
PhD student of Biophysics Dept.

Nanjing University


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