Hi,
the general assumption is that having one or two fast vibrations un-SHAKED
(as opposed to tens of thousands in non-SHAKE water solvation) will have
little impact on your simulation. Depending on the actual system at hand,
you have to check that this very localized integrator inaccuracy does not
mess with your structure and dynamics.
As far as energy conservation goes, do you see a difference between 1fs
and 2fs timestep TI-MD runs? If you are using a thermostate, this should
not be noticeable.
Thomas
On Wed, November 2, 2011 8:36 am, Peter Winn wrote:
> Dear Amber Users,
>
> In Softcore TI SHAKE is switched off for unique-atom to common atom bonds,
> yet as far as I can see people are still using 0.002ps time steps rather
> than changing to 0.001ps.
> Is this just a case that if the simulations are stable this is fine. Are
> there no other issues such as energy conservation?
> Any thoughts and comments are welcome.
>
> Many thanks
>
> Peter Winn.
>
>
> Peter James Winn
> RCUK Roberts Fellow
> Centre for Systems Biology
> University of Birmingham
> Tel: +44 (0)121 414 8852
> Fax: +44 (0)121 414 8844
> p.j.winn.bham.ac.uk
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Nov 02 2011 - 07:30:05 PDT
