Dear Amber users,
I am trying to simulate a DNA system with Amber16 sander.MPI ,it gives a
problem in the equilibration .
The process is aborted with terminal error displayed as :
" *MPI_ABORT was invoked with rank 0 in communicator MPI_COMM_WORLD with
errorcode 1* "
I went through the output files of the system and found error as stated in
the header of this mail.
I have gone through the Amber mailing list and relevant to error written .
Accordingly I tried using my system with ntp=0;ntb=1 in the input file but
the error continued to occur .
Error in .out file is :
" *Coordinate resetting (SHAKE) cannot be accomplished, deviation is too
large NITTER,NIT,LL and J are 0 1 151 436 437* "
And failed to generate .rst files, .crd files
Looking into the atom numbers in the error I found that the atoms donot
pose much of steric hinderance to the system.
The contents of my initial input file are as follows :
"
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000, nmropt=1
/
&wt type='DUMPFREQ', istep1=1 /
&wt type='END' /
DISANG=res1
DUMPAVE=test.dat
LISTIN=POUT
LISTOUT=POUT
Keep DNA fixed with weak restraints
10.0
RES 1 18
END
END "
Kindly share your suggestions upon the problem !
Thank you in advance and regards,
Kripi Tomar
IIT Hyderabad
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Received on Thu Feb 22 2018 - 23:30:02 PST
