Did you do any minimization/equilibration prior to your production run?
-Dan
On Thu, Sep 22, 2016 at 11:49 AM, ABHIJEET CHOWDHURY
<f2013854.pilani.bits-pilani.ac.in> wrote:
> Dear AMBER users,
>
> I am trying to simulate a 22 mer RNA duplex in an implicit solvent. After
> few 100 picoseconds, SHAKE gets unstable and is unable to restrain the
> structure. The message displayed on screen suggests this may due to some
> deeper energitics problem. Can someone suggest where should I look for the
> problem.
>
> Thank You
>
> Regards,
> Abhijeet Chowdhury
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Sep 22 2016 - 09:00:04 PDT
