From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Nov 19 2019 - 14:21:53 CST
ref {
dummyAtom (0.0, 0.0, 0.0)
}
On Tue, Nov 19, 2019 at 2:20 PM Jiali Wang <jwang204_at_binghamton.edu> wrote:
> Dear NAMD users,
> Good afternoon,I have trouble in collective variable, when i am collecting
> Z positions in Colvars. I found the distance collected is from main
> atomnumbers to ref atomnumbers. But what I want to collect is absolute Z
> positions (like reference atom is (0,0,0)), Do you know how to set this? I
> try to use dummyatom as reference atom, it can't recognize it. and if I
> make anychange, does it affect harmonic constant part?
> Thank you for your time.
> Jiali
>
> here is my colvars file.
> colvar {
> name length
> lowerboundary -19.0
> upperboundary 10.0
>
> lowerwallconstant 100.0
> upperwallconstant 100.0
>
> outputAppliedForce off
> distanceZ {
> main {
> atomNumbers 19021}
> ref {
> refPositions (0.0, 0.0, 0.0)}
> axis ( 0.0, 0.0, 1.0 )
> }
> }
> harmonic {
> name lenZ
> colvars length
> forceConstant 1 # in kcal/mol/A^2
>
> centers -1.0 # go from 25 Angstrom RMSD...
>
> outputCenters on
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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