Re: colvar with moving frame of reference

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Mon Apr 16 2018 - 14:24:41 CDT

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
> }
>
>
>
>

This archive was generated by hypermail 2.1.6 : Sun Sep 15 2019 - 23:19:35 CDT