Hi Kevin,
Having a negative sign in ntwr is fine (see p.26 of the manual) --
this just writes out separate restart files every N steps instead of
overwriting a single restart file every N steps. This can actually be
a useful thing to do on occasion...
Best,
Paul
On Sep 28, 2010, at 9:38 AM, Kevin Hauser wrote:
> 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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>> 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 - 11:00:04 PDT
