Re: Rotate two linked proteins against each other and calculate energy profile

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Mar 28 2011 - 16:46:29 CDT

On Mon, Mar 28, 2011 at 20:43, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> On 28 March 2011 18:18, Bjoern Olausson <namdlist_at_googlemail.com> wrote:
>> It looks like this would solve the problem but:
>> colvars:   Error: keyword "wraparound" is not supported, or not recognized in
>> this context.
>
> That is because wrapAround is an option of the component, not the
> colvar; it belongs inside the dihedral {} block. The reason for this
> is, with a component such as dihedral, the code knows where it stands
> with respect to periodicity. Since colvars can be complicated
> combinations, there is not much the code can do on a very general
> basis, so all the periodic treatment is done at the component level.
>

Hi again,

I was a bit fast with my last reply. NAMD accepted the wrapAround
keyword in the dihedral block, but the results are still the same as
without using "wrapAround 180" when using 0 to 360 degrees instad of
-180 to 180:
ethane_0_to_360.png (looks the same with and without wrapAround 180)
http://ompldr.org/vODAzbw/ethane_0_to_360.png
ethane_-180_to_180.png
http://ompldr.org/vODAzcA/ethane_-180_to_180.png

colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = eprof
colvars: Initializing a new "dihedral" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 180
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass = 1.008.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
colvars: Initializing atom group "group3".
colvars: Atom group "group3" defined, 1 initialized: total mass = 12.011.
colvars: Initializing atom group "group4".
colvars: Atom group "group4" defined, 1 initialized: total mass = 1.008.
colvars: All components initialized.
colvars: # width = 1
colvars: # lowerBoundary = 0
colvars: # lowerWallConstant = 10
colvars: # lowerWall = 0 [default]
colvars: # upperBoundary = 360
colvars: # upperWallConstant = 10
colvars: # upperWall = 360 [default]
colvars: Lower wall and upper wall are equal in the periodic domain
of the colvar: disabling walls.
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = on
colvars: # outputAppliedForce = on
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------

Cheers,
Bjoern

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