From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Dec 03 2013 - 16:07:12 CST
Yes, that is right.
Giacomo
On Tue, Dec 3, 2013 at 4:57 PM, Kasra Fattah <kasra.fattah_at_gmail.com> wrote:
> Jerome,
> Using "distnaceXY" and assuming that I want the molecule to remain within
> e.g. 5 from the ref point, how should I use the "upperWall" and "lowerWall"
> values? Is that just: "upperwall 5"? As I understand "distanceXY" colvar is
> a norm and is just positive so I can only use positive values for
> "upperWall" and "lowerWall" right?
>
> Cheers,
> Kasra.
>
>
> On Tue, Dec 3, 2013 at 12:39 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>wrote:
>
>> The natural complement to distanceZ for such a case is distanceXY. You
>> can restrain that.
>>
>> Jerome
>>
>> ----- 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?
>>
>> > Cheers,
>> > Kasra.
>>
>> > 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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