Re: COLVAR metadynamics: center of mass of atoms crossing simulation box

From: Lorenz Ripka (
Date: Fri May 23 2014 - 07:35:23 CDT


thanks a lot for your hint. it would be very helpful, if forceNoPBC
would be available in the next release for angles and dihedrals, too.
How long do you think will this take?

kind regards,


On 05/20/2014 06:41 PM, Giacomo Fiorin wrote:
> Hello Lorenz, the centers of mass of the groups are always calculated
> without PBCs (hence the need to disable wrapAll in many cases), but
> mutual distances between the centers are instead calculated with PBCs.
> This hasn't happened frequently before, but if you need it we can
> probably add the forceNoPBC feature used in the distance-based
> variables to angle and dihedrals as well in the coming release.
> Giacomo
> On Mon, May 19, 2014 at 8:17 AM, Lorenz Ripka
> < <>>
> wrote:
> 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
> this situation?
> Kind regards

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