[gmx-users] Exploding poly-serine

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 27 05:00:23 CEST 2009

Warren Gallin wrote:
> David,
>     That is probably it, I had a 2-femtosecond step and no bond 
> constraints.  Obviously I need to read up on the pros and cons of the 
> various restraint regimes.
>     I guess that would be consistent with the sudden explosion after 
> along period of stable running.
>     Why poly-Ser would be more susceptible to this than poly-Pro, 
> poly-Asp or poly-Gly is not obvious to me, but I am sure that there is a 
> reason out there somewhere.

If this is the cause, the difference in numerical stability may well not 
be caused by the difference in the residue (i.e. the physical model) but 
in the initial conditions.


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