Hello. I am running TI calculations with and without softcore and I have
noticed that once I turn softcore off, the simulation crashes before it
even starts. The only error message I get is
[bohr107:26692] *** An error occurred in MPI_Sendrecv
[bohr107:26692] *** on communicator MPI COMMUNICATOR 4 SPLIT FROM 0
[bohr107:26692] *** MPI_ERR_TRUNCATE: message truncated
[bohr107:26692] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
--------------------------------------------------------------------------
mpirun has exited due to process rank 4 with PID 26692 on
node bohr107 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
The two systems differ only by the absence of a hydrogen atom (it is a pka
type of simulation). Here is the input for one of them:
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
cut = 9.0,
noshakemask = ':342',
ntr = 0,
ntc = 2,
ntf = 1,
temp0 = 298.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 1000000, dt = 0.0005, ntave = 100,
ntpr = 100, ntwx = 100, ntwr = 100,
ig = 10704, ioutfm = 1, iwrap = 1,
icfe = 1, ifsc = 1, clambda = 0.04691,
ifqnt = 0, scmask = ':342', idecomp = 1, nmropt = 0,
/
Receptor residues
RRES 1 7853
END
Printing
RES 1 342
END
END
Once I turn ifsc = 0 and erase the scmask, the simulation does not run.
Writing the crgmask = ':342.H2' also does not help.
Am I doing something wrong here?
Thank you
Fabrício
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Received on Tue Feb 26 2013 - 15:30:03 PST
