Re: Re: metadynamics simulations slow down and down

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Mon Oct 11 2010 - 11:47:44 CDT

Hello Cheng, not knowing how your system is or your choice of colvar, I have
to guess.

You used a relatively large wall force constant (500 kcal/mol per unit of
the colvar). Can it be that the application of a very strong wall force has
perturbed the configuration of the system in an irreversible way? In that
case, it may happen that a minimum appear where you don't think there could
be one, because the other degrees of freedom (i.e. all but the colvar) are
not at the equilibrium any more.

Giacomo

---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
  giacomo.fiorin_at_temple.edu
---- ----

2010/10/11 OiniL <noinil_at_gmail.com>

> 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
> ns.
> 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
>
>
> --
>
> ---------------------------------------------------------------------------------
> ף
>
>
> ̷ة
>

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