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.
Thanks,
Warren Gallin
On 26-Aug-09, at 10:48 AM, David van der Spoel wrote:
[Details deleted]
So my questions are:
1) Am I missing some obvious step in setting up a stable
simulation?
2) Is it true that the high internal force present at the end of
the initial energy minimization could be the root of the problem?
3) If so, is there an obvious method for relaxing the system
into a more stable state prior to the main MD run?
What time step are you using? Since you are not using bond-
constraints the time step should be on the order of 0.5 fs.
Warren Gallin
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University.
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