Dear friends,
I am running a simulation of DNA with amber11 pmemd.cuda (MPI).
As I started saving trajectories in binary format with ioutfm = 1, the
job ran well for 1 ns but its
not able to restart the job in next step.
Job is getting killed with the message
" *forrtl: severe (174): SIGSEGV, segmentation fault occurred* "
when I tail the restart file I got
NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN
NaN NaN NaN
226.7152699 226.7152699 226.7152699 109.4712175 109.4712175 109.4712175
Here is the input file.
NVT dynamics for DNA, 9.0 cut
&cntrl
nmropt = 0,
ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
ntwprt = 0, ntwr = 500,
ntf = 2, ntb = 1, dielc = 1.0,
cut = 9.0, nsnb = 10,
ipol = 0,
ibelly = 0, ntr = 0,
imin = 0,
maxcyc = 5000,
ncyc = 2000,
ntmin = 1, dx0 = 0.1, dxm = 0.5, drms = 0.0001,
nstlim = 500000
nscm = 1000,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 10.0,
ig = 71277, heat = 0.0,
ntt = 1, dtemp = 0.0,
ioutfm = 1
ioutfm = 1
tautp = 1.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 0.5,
ntc = 2, tol = 0.0005,
&end
&ewald
a = 62.9065214, b = 46.8818659, c = 192.6251811,
&end
Have anyone faced the same problem before, if yes please share your
solution.
*
*
--
*With Regards,
HIMANSHU JOSHI
Graduate Scholar, Center for Condense Matter Theory
Department of Physics IISc.,Bangalore India 560012*
ॐ सर्वे भवन्तु सुखिनः सर्वे सन्तु निरामयः।
सर्वे भद्रणिपश्यन्तु मा कश्चिद्दुःख भाग भवेत्॥
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Received on Thu Jul 12 2012 - 23:00:03 PDT
