The negative sign is used to generate RST file during production run. One rst file at the end of simulation ( *.rst_100000) and another one in intermediate (*.rst_50000). I have been using this for some time.
Thank you.
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
--- On Wed, 29/9/10, Kevin Hauser <84hauser.gmail.com> wrote:
> From: Kevin Hauser <84hauser.gmail.com>
> Subject: Re: [AMBER] running pmemd fails
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Wednesday, 29 September, 2010, 0:38
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -- - -
> 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 - 20:00:04 PDT
