From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Dec 03 2013 - 12:39:25 CST
The natural complement to distanceZ for such a case is distanceXY. You can restrain that.
----- Mail original -----
> Thanks for your response Jerome.
> I also tried using "period" and "wrapAround" options with "period 50" and
> "wrapAround 0.0" (basically the default value of wrapAround) in distanceZ
> and I used the unwrapped coordinates for the walls positions, i.e.
> "lowerWall 20" and "upperWall 30". It seems that it's working too, is that a
> legit treatment of the problem or not? (btw, I'm using a dummy atom as a
> reference group at position (0.0, 0.0, 0.0) )
> One more question:
> I'm actually doing a 1D ABF calculation and my reaction coordinate is Z
> direction of the cartesian system. But in order to limit the simulation in x
> and y directions I'm defining two other reaction coordinates, x and y. The
> sole application of these two reaction coordinates are for using their
> "lowerWall" and "upperWall" options to enforce the molecule remains in the
> desired window in x and y directions but I'm not using them in free energy
> calculation part of abf, i.e. just using "colvars z" in the abf part of the
> config file. I was wondering if this is a right way of confining the
> molecule in the directions that I'm not doing free energy calculations?
> On Sat, Nov 30, 2013 at 7:04 PM, Jérôme Hénin < jerome.henin_at_ibpc.fr > wrote:
> > Hi Kasra,
> > The best way for this is to use distanceZ with a reference group close to
> > the
> > region of interest (if you want an absolute position along the axis, it
> > would be a dummy atom group, and you can choose its position arbitrarily).
> > In the case you describe in your message, you could define a distanceZ
> > component with the reference group as a dummy atom at (0, 25, 0), in which
> > case the lowerWall would be -5 and upperWall would be 5. You don't need to
> > worry about PBC, as they will be enforced automatically, because the
> > distance between your molecule and the dummy atom will be computed
> > following
> > the minimum image convention.
> > That's why the distanceZ coordinate is not explicitly treated as periodic
> > by
> > default: the minimum image convention for distances usually does the job
> > well.
> > Cheers,
> > Jerome
> > > Hi All,
> > > I've got a question regarding the treatment of a reaction coordinate that
> > > crosses a periodic boundary.
> > > If I want to confine the center of mass of a molecule between two points
> > > along, let's say, y axis which crosses the periodic boundary in that
> > > direction how should I define lowerWall and upperWall? for example if the
> > > box size in y direction is from -25 to 25 and initially the com of the
> > > molecule is located at y=25 but I want it to be confined in y-direction
> > > +/-
> > > 5 from its initial position. Based on unwraped values it should be
> > > between
> > > 20 and 30, i.e. "lowerWall 20" and "upperWall 30" but I'm not sure if I
> > > have
> > > to use unwrapped coordinates or wrapped ones?!
> > > I Would appreciate it if you could help me to know how I should set these
> > > values...There are also two options in the manual "period" and
> > > "wrapAround"
> > > should I also set them (i.e. "period 10" and "wrapAround 25")? or they
> > > are
> > > not related to what I need?
> > > Cheers,
> > > Kasra.
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