Re: failure in RATTLE algorithm using the adaptive biasing force method

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Tue Nov 11 2008 - 14:52:19 CST

Hi Steve, which is the value of that dihedral in the starting
configuration? It might be that the system is initially far outside
of the window you've chosen. In that case, the boundary force which
is applied to make it stay within the window is just too large. If
that is what's happening, you should pick a configuration that falls
within the window to start the simulation. Since you've completed a
run with the whole -180:180 range, you should have plenty of them for
whatever window you define.

Giacomo

---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
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---- ----

On Tue, Nov 11, 2008 at 2:43 PM, <steve.kaminski_at_mail.tu-berlin.de> wrote:
> Dear all.
>
> My aim is to calculate a PMF of a certain molecule as a function of a
> dihedral angle. Therefore, I use the adaptive biasing force method. As long
> as I scan the complete dihedral space (xiMin=-180 / xiMax=180) the
> calculations run without problems. But in my case I just want to scan a
> reduced space, so if I change the values e.g. of xiMin to -100 or any other
> value, I get immediately the following error message from NAMD:
>
> Warning: Constraint failure in RATTLE algorithm for atom 19
> Warning: Constraint failure in RATTLE algorithm for atom 22
>
> If I turn off rigidBonds in the NAMD config-file I receive the following
> error:
>
> ERROR: Atom 20 velocity is 1050.76 -3548.3 -5428.46 (limit is 5000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely.
>
> Thank you very much in advance for your suggestions.
>
> Steve
>
>

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