Re: colvar with moving frame of reference

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Tue Apr 17 2018 - 13:39:23 CDT

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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