Re: colvar with moving frame of reference

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Apr 16 2018 - 15:03:08 CDT

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#
SECTION0001341240000000000000.

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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