From: Lorenz Ripka (l.ripka_at_gmx.de)
Date: Mon May 19 2014 - 03:44:36 CDT
We are performing metadynamics calculations using as collective
variables (CV) an angle and a dihedral angle, defined using the centers
of mass of several atoms of our protein complex (i.e. some of the groups
of atoms span different molecules).
The simulations proceed as expected until some of the atoms defining the
CVs cross the periodic boundaries of the simulation box. When this
happens large jumps are observed in our CVs.
Our guess is that the centers of mass of the sets of atoms, used to
define the angles, are computed AFTER wrapping their coordinates in the
simulation box, thus resulting in sudden changes of their coordinates as
the atoms cross the box boundary.
This occurs even if we set wrapAll off. Indeed in the dcd files the
coordinates of the complex are not wrapped.
Can someone suggest a method to prevent this from happening or to solve
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