RE: colvar with moving frame of reference

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Apr 16 2018 - 14:08:06 CDT

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 22 2019 - 23:19:30 CDT