my simulation does not dies off ,,,it only shows these messages at
nearly 50 ps and then continues..
my result with serial is almost same as that with parallel
but should i continue with these errors/ messages...what should be
the remedy'''
i tried varying restraint from 10 to 2 kcal. also i checked with
dt= 0.001 and 0.002...but things are not going ..
On 9/4/12, Dr. Vitaly Chaban <vvchaban.gmail.com> wrote:
> You did not mention how long your simulation lasls. I would at least
> wait for 1.0 ns ... and then if the problem does not disappear
> silently, start panic.
>
>
> Dr. Vitaly V. Chaban
>
>
>
>
> On Tue, Sep 4, 2012 at 1:12 PM, najmul arfin <syednajmularfin.gmail.com>
> wrote:
>> dear users,
>> my problem is..
>> when i am using NVT for rasising temperature in serial version of
>> AMBER everything is fine but when i am using parallel version with 8
>> processors..i am getting messages like
>> ***** Processor 2
>> ***** System must be very inhomogeneous.
>> ***** Readjusting recip sizes.
>> In this slab, Atoms found: 6221 Allocated: 5760
>>
>> ***** Processor 5
>> ***** System must be very inhomogeneous.
>> ***** Readjusting recip sizes.
>> In this slab, Atoms found: 6499 Allocated: 5760
>>
>> though md.out file seems to be okay and i don't see any vaccum/bubbles..
>>
>> so what can be the possible reason ..or how it can be resolved....or
>> should i take these msg normally due to distribution of jobs
>>
>> my input file is:
>> &cntrl
>> imin = 0,
>> irest = 0,
>> ntx = 1,
>> ntb = 1,
>> cut = 10,
>> ntr = 1,
>> ntc = 2,
>> ntf = 2,
>> tempi = 0.0,
>> temp0 = 300.0,
>> ntt = 3,
>> gamma_ln = 1,
>> nstlim = 100000, dt = 0.001
>> ntpr = 100, ntwx = 100, ntwr = 1000
>> /
>> Keep DNA fixed with weak restraints
>> 2.0
>> RES 1 96
>> END
>> END
>>
>>
>>
>>
>> --
>> NAJMUL ARFIN
>> Research Scholar
>> SCHOOL OF PHYSICAL SCIENCES,
>> JAWAHARLAL NEHRU UNIVERSITY,
>> NEW DELHI -110067
>> +919910040525
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
NAJMUL ARFIN
Research Scholar
SCHOOL OF PHYSICAL SCIENCES,
JAWAHARLAL NEHRU UNIVERSITY,
NEW DELHI -110067
+919910040525
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Received on Tue Sep 04 2012 - 07:00:02 PDT
