From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Apr 21 2011 - 06:30:47 CDT
Hi Giacomo,
> You have dummy atoms in the dihedral definitions, which stay fixed in
> space. The rest of the system, however, can drift under the effect of the
> PME truncation error, Langevin forces, etc as you know already. Do the
> other atoms fly very far away from the dummy ones? Maybe that could be why
> you get the dihedrals out of control?
>
> The backbone atoms of the helix are constrained, so the system can not
drift. (The part of the backbone where the label is attached is not
constrained, so that hopefully the orthogonality of colvars and constraints
is OK.
I tried changing the values of the coupling
extendedFluctuation 3
extendedTimeConstant 80
With this end result<http://www.ijs.si/ijs/dept/epr/ajasja/mails/ABF/crash2.gif>
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