[gmx-users] Exploding poly-serine
wgallin at ualberta.ca
Wed Aug 26 19:30:18 CEST 2009
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.
On 26-Aug-09, at 10:48 AM, David van der Spoel wrote:
>> So my questions are:
>> 1) Am I missing some obvious step in setting up a stable
>> 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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> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
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