From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Wed Sep 02 2020 - 07:28:03 CDT
Hello,
I am performing some steered molecular dynamics simulations. I was
wondering how the harmonic biases worked.
I understand how a simple colvar with a harmonic bias on the distance
between atoms could work. I can picture it as a spring attached
between the atoms which exerts a force that pulls each atom towards
the other.
However, for more complicated colvars such as radius of gyration,
coordination number, dihedral angle, RMSD, to name a few, how exactly
does the added potential manifest itself to restrain these quantities
to their desired values? In which direction do the forces/springs
point (or are there even forces at all) if I put a harmonic bias on
these colvars?
I have looked at the user guide and the Colvars paper, but I am still
confused about the forces.
If anyone could help me clear this up or point me in the right
direction with some references, that would be greatly appreciated.
Thank you very much,
Mortimer
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