Hello. I am using amber12 (fully patched) to perform TI calculations. I am
having somoe problems related to the number of processors used for the
calculation. Everytime I choose set -np bigger than 8, the calculation
starts with the warning:
***** Processor 0
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 6266 Allocated: 6094
(this is for a -np 16 calculation)
The simulation seems to continue, regardless of the warning. I found a
thread that deals with a similar problem, but it is not related to TI
calculations. In this thread, the user was advised to change the ntc and
ntf values. The only combination that works for me is ntc = 2 and ntf = 1.
I was wondering if there is an unwritten limitation to the number of
processors that can be used for a ti simulation.
My mdin file for V0 is given below.
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
cut = 8.0,
ntr = 0,
ntc = 2,
ntf = 1,
temp0 = 298.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 1000000, dt = 0.002, ntave = 1000,
ntpr = 1000, ntwx = 1000, ntwr = 1000, ntxo = 2,
ig = 10703, ioutfm = 1, iwrap = 1,
icfe = 1, ifsc = 1, clambda = 0.02544,
noshakemask = ':342', scmask = ':342.H2', idecomp = 1, nmropt = 0,
/
Receptor residues
RRES 1 7102
END
Printing
RES 1 342
END
END
Thank you
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Received on Wed Sep 18 2013 - 13:30:02 PDT
