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

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Mar 29 2011 - 07:03:14 CDT

Hi Bjoern,

Thanks for your report, you did find a bug. The attached source files fix it.

Cheers,
Jerome

On 28 March 2011 23:46, Bjoern Olausson <namdlist_at_googlemail.com> wrote:
> 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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