From: Jackson Cavett (
Date: Mon Jun 27 2016 - 19:11:05 CDT

Hello All,

I am relatively new to NAMD and had a question regarding speeding up a
simulation. I need to run an equilibration for 40-50 nanoseconds due to the
large number of atoms in the molecule I am using. The molecule is integrin
AlphaVbeta3. Right now I have a simulation running for about 25 million
timesteps with a timestep value of 2.0. I attempted to increase the
timestep, but ran into the "constraint failure rattle algorithm" error,
which I know usually results from a timestep that is too large. I was
wondering: is there a way to speed up a simulation somehow? Is there a way
to increase the timestep without creating an error?

Thank you all in advance for your help.