Re: colvar with moving frame of reference

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Apr 17 2018 - 16:18:29 CDT

Hi Dhiraj,

the axis vector should be provided in the frame of the reference
coordinates (here, reference.pdb). If you load reference.pdb and calculate
the principal axes of the helix of interest, that should be correct. There
is no translational reference or origin needed, as it is describes a
translation-invariant direction. It's sensitive only to rotations.

There is no need to normalize the vector, that's done internally - anyway
the vector you have seems normalized already.

Jerome

On 17 April 2018 at 20:39, Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:

> Thanks Giacomo
> based on your suggestion, I figured it out how to
> do it. I made it like the below script and it seems to be working however I
> am getting kink in my helix. I don't know if its real or I am making any
> mistake in defining the helical axis. for the axis definition, what should
> be the vector? I am using measure inertia command in vmd and using the
> vector that I am getting as it is. do I need to convert it to with respect
> to the geometric centre of my helix. because I believe the vector I am
> getting is in the context of origin. Do I need to normalize the vector ?
>
> Thanks
> Dhiraj
>
>
> colvar {
> name spin
> outputAppliedForce on
> spinAngle {
> atoms {
> atomsFile spin.pdb
> atomsCol B
> atomsColValue 1
> centerReference yes
> rotateReference yes
> fittingGroup {
> psfSegID AP1
> atomNameResidueRange CA 29-211
> }
> refPositionsFile reference.pdb
> refPositionsCol B
> refPositionsColValue 1
> }
> refPositionsFile spin.pdb
> refPositionsCol B
> refPositionsColValue 1
> axis (-0.22284841537475586,
> 0.4576619863510132, 0.8607462048530579)
> }
> }
>
> harmonic {
> name harm
> colvars spin
> forceConstant 1000 # kcal/mol/deg^2
> centers 0
> targetCenters -90
> targetNumSteps 1000000
> }
>
>
>
> On Mon, Apr 16, 2018 at 3:03 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Dhiraj, it looks like you're trying random modifications to this
>> template:
>> http://www.ks.uiuc.edu/Research/namd/2.12/ug/node57.html#SEC
>> TION0001341240000000000000.
>>
>> You can't define multiple groups with the same name in the same variable
>> component. SpinAngle only requires one group called "atoms", and you may
>> optionally define fittingGroup inside it.
>>
>> The documentation for spinAngle is here:
>> http://colvars.github.io/colvars-refman-namd/colvars-refman-
>> namd.html#sec:cvc_spinAngle
>>
>> And the one for fittingGroup is here:
>> http://colvars.github.io/colvars-refman-namd/colvars-refman-
>> namd.html#sec:colvar_atom_groups_ref_frame
>>
>> Giacomo
>>
>> On Mon, Apr 16, 2018 at 3:24 PM, Dhiraj Srivastava <dhirajks_at_gmail.com>
>> wrote:
>>
>>> Hi Josh
>>> Sorry I send everyone wrong script. this is the once which is
>>> showing the error "colvars: Error: keyword "refpositionsfile" is not
>>> supported, or not recognized in this context."
>>> olvar {
>>> name spin
>>> outputAppliedForce on
>>> spinAngle {
>>> atoms {
>>> atomsFile spin.pdb
>>> atomsCol B
>>> atomsColValue 1
>>> refPositionsFile spin.pdb
>>> refPositionsCol B
>>> refPositionsColValue 1
>>> axis (-0.47851067781448364,
>>> 0.23966480791568756, 0.8447416424751282)
>>> }
>>> atoms {
>>> psfSegID AP1
>>> atomNameResidueRange CA 212-220
>>> centerReference yes
>>> rotateReference yes
>>> fittingGroup {
>>> psfSegID AP1
>>> atomNameResidueRange CA 1-211
>>> }
>>> refPositionsFile spin.pdb
>>> }
>>> }
>>> }
>>> harmonic {
>>> name harm
>>> colvars spin
>>> forceConstant 16200 # kcal/mol/deg^2
>>> centers 0
>>> targetCenters -90
>>> targetNumSteps 10000000
>>> }
>>>
>>>
>>> Thanks
>>> Dhiraj
>>>
>>>
>>> On Mon, Apr 16, 2018 at 2:08 PM, Vermaas, Joshua <
>>> Joshua.Vermaas_at_nrel.gov> wrote:
>>>
>>>> Hi Dhiraj,
>>>>
>>>> Why are there three "atoms" declarations inside the spinAngle?
>>>> Admittedly I haven't looked into the source to see if this is legal syntax,
>>>> but I don't think that it is.
>>>>
>>>> -Josh
>>>>
>>>>
>>>>
>>>> On 2018-04-16 12:34:27-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>>>>
>>>> Hi
>>>> I am trying to use the spinAngle colvar and using the moving frame
>>>> of reference. however namd is showing error that
>>>> "colvars: Error: keyword "refpositionsfile" is not supported, or not
>>>> recognized in this context."
>>>>
>>>> how should I solve this problem?
>>>>
>>>> thank you
>>>> Dhiraj
>>>>
>>>>
>>>> my colvar script is
>>>>
>>>> colvar {
>>>> name spin
>>>> outputAppliedForce on
>>>> spinAngle {
>>>> atoms {
>>>> atomsFile spin.pdb
>>>> atomsCol B
>>>> atomsColValue 1
>>>> refPositionsFile spin.pdb
>>>> refPositionsCol B
>>>> refPositionsColValue 1
>>>> axis (-0.47851067781448364,
>>>> 0.23966480791568756, 0.8447416424751282)
>>>> }
>>>> atoms {
>>>> CenterReference on
>>>> RotateReference on
>>>> refPositionsFile spin.pdb
>>>> refPositionsCol B
>>>> refPositionsColValue 1
>>>> }
>>>> atoms {
>>>> psfSegID AP1
>>>> atomNameResidueRange CA 212-220
>>>> centerReference yes
>>>> rotateReference yes
>>>> fittingGroup {
>>>> psfSegID AP1
>>>> atomNameResidueRange CA 1-211
>>>> }
>>>> refPositionsFile spin.pdb
>>>> }
>>>> }
>>>> }
>>>>
>>>> harmonic {
>>>> name harm
>>>> colvars spin
>>>> forceConstant 16200
>>>> centers 0
>>>> targetCenters -90
>>>> targetNumSteps 10000000
>>>> }
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>

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