AMBER Archive (2006)

Subject: RE: AMBER: SHAKE, TIP3P and 2fs Timesteps

From: Ross Walker (
Date: Wed May 31 2006 - 12:56:31 CDT

Hi Mark,

> It is my understanding that the TIP3P water model has the O-H bond
> restrained (frozen), hence to use this as a solvent in a model, SHAKE
> should really be used.
> Is this correct? What artifacts may be introduced by running a
> simulation with TIP3P solvent without SHAKE?

Others may be able to comment more here but I believe that since TIP3P was
parameterised to be used with shake using it without shake, even with a
short time step, can result in incorrect densities, radial distribution
functions etc. I don't know how large these errors are however or how large
the overall implications would be. You may want to consider using one of the
flexible water models such as SPCFW.

On an aside I believe a number of people now consider 2fs with shake to
really be on the bleeding edge of what you can safely use. This is with
regards to energy conservation etc when running in the NVE ensemble. For
safety you should probably use a 1.5fs timestep even with shake.
> As a side question from this, what artifacts may be introduced by
> running a simulation with SHAKE enabled but using 1fs timesteps?

None other than your computational budget...

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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