VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 28 2016 - 10:15:00 CDT

Hi,
  Numerical integration of dynamics (of any kind) is only stable when
the integration timestep is shorter than the fastest vibrational mode
present in the system being simulated. In the case of all-atom MD this
means you have to have a timestep short enough to capture the motions of
the lightest atoms with the fasted vibrations, hydrogens. You can't simply
make the timestep larger unless (complicated) schemes are used to handle
the modeling of hydrogens in a different way. This means that
a 2.0fs timestep is normally the upper bound in NAMD at present.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 27, 2016 at 07:11:05PM -0500, Jackson Cavett wrote:
> 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.
> Jack 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/