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From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Mon Jun 27 2016 - 19:11:05 CDT
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.