velocity error during steered MD

From: Markus K. Dahlgren (
Date: Tue Apr 26 2011 - 09:08:32 CDT

Dear NAMD users,

Has anyone encountered velocity errors during steered MD, and if so how can it
be handled?

I have a system of a protein complexed with a ligand and the protein is highly
flexible. I equilibrated the whole system for 21ns, using 1fs integration, and
then started my SMD pulling. But I noticed that the protein had significant
center of mass movement so I redid the solvation and ionization, put in 5
harmonic constraints (1kcal force constants) to prevent center of mass
movement, then equilibrated the system for 16ns. I resume the pulling at 10 or
25 A/ns and after a few hundred ps I get velocity errors of some water
molecules. The ligand-protein binding is significant and the ligand has not
moved at all away from the binding pocket before the velocity errors show up.

During SMD, the thermostat is turned off. Are the velocity errors more frequent
as a result of having no thermostat? Can velocities be controlled by using some
other configuration parameters, such as temperature rescaling? Or is my only
option to equilibrate it long enough to remove these errors?

Thank you in advance for any insight you can offer!

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