On Tue, Sep 28, 2010, Vijay Manickam Achari wrote:
>
> I have have been using AMBER10 for my simulation. For the equilibrium
> process I use sander.MPI and for the production process I tried to use
> PMEMD. What is happening is the simulation terminates immediately upon
> submitted. The message in the output file is as below:
>
> | Running AMBER/MPI version on 64 nodes
Try it on fewer nodes, just to check.
>
> Coordinate resetting (shake) was not accomplished
> within 3000 iterations
Shake failure are usually symptoms of other underlying problems. Try a
20-step run witn ntpr=1, using both sander and pmemd. See if you can track
down what the differences are.
....dac
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Received on Tue Sep 28 2010 - 05:00:09 PDT
