According to Case's advice, I have tried to run small number of steps using fewer nodes. It runs in 16 nodes but more than this number it terminates indicating the same problem about as shake.
Why this happens and where the mistake could be?
If I run using sander.MPI, 64 nodes can be used and , it doesn't show any error.
Is there any suggestion for this issue?
Thank you.
Vijay.M
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
--- On Tue, 28/9/10, case <case.biomaps.rutgers.edu> wrote:
> From: case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] running pmemd fails
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Tuesday, 28 September, 2010, 19:55
> 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 - 21:00:04 PDT
