There appears to be a negative sign in ntwr, see below.
&cntrl
imin=0,
irest=1, ntx=5,
scnb=1.0, scee=1.2,
iwrap = 1, nscm=1000,
ntt=2, temp0=348.0, tautp=1.0,
ntb = 2, ntp=1, taup=0.2,
ntf=2,ntc=2,
nstlim=100000, dt=0.001,
ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
this ought to be "ntwr = 50000"
cut = 9.0
/
HTH,
kevin
On Tue, Sep 28, 2010 at 7:55 AM, case <case.biomaps.rutgers.edu> wrote:
> 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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>
--
-- - -
HK
-------------------------------------------------------
Kevin Eduard Hauser
National Science Foundation,
LSAMP Bridge to the Doctorate Fellow
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
Phone: (561) 635.1848
Email: 84hauser.gmail.com
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Received on Tue Sep 28 2010 - 10:00:04 PDT
