YES.
You should peacefully wait for at least 1 ns (time depends totally on
the system, say on its shear viscosity). If the problem does not
vanish, than it is worthwhile to discuss what happens.
Everything can happen during initial equilibration... The fact that
you do not notice the vacuum visually, does not mean that your system
is super relaxed.
Dr. Vitaly V. Chaban
On Tue, Sep 4, 2012 at 3:46 PM, najmul arfin <syednajmularfin.gmail.com> wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> 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
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
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Received on Tue Sep 04 2012 - 07:00:02 PDT
