MD with 3-site CO model

From: Nadia Elghobashi-Meinhardt (
Date: Wed Mar 04 2020 - 08:24:51 CST

Hi everyone,
I am using a 3-site CO model (of Straub&Karplus, with a dummy atom of zero
mass) with the charmm36ff to simulate the diffusion of a rigid CO molecule.
I am not sure of what combination of force constants / constraints/ heating
protocols to use.
With my current setup, NAMD complains of high velocities for the dummy atom.
Does anybody have any tips?
Thank you!

Technical University Berlin

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