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
>
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Received on Tue Sep 04 2012 - 06:00:02 PDT
