From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Tue Nov 19 2019 - 14:27:41 CST
Just set the coordinate of atom 19021 in the reference pdb to 0,0,0? Sounds simple enough.
On Tue, Nov 19, 2019 at 1:52 PM Jiali Wang <jwang204_at_binghamton.edu<mailto: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.
here is my colvars file.
refPositions (0.0, 0.0, 0.0)}
axis ( 0.0, 0.0, 1.0 )
forceConstant 1 # in kcal/mol/A^2
centers -1.0 # go from 25 Angstrom RMSD...
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