Hi Bill,
I am using Amber10, to perform TI calculations for decharging and removing
vanderwaals, for the substrate molecule(under periodic boundary conditions,
and using explicit model). The equilibration process was done by using
Amber8. I am unable to execute TI calcuations using Amber10. The following
is the input and test.group file
input file (both for decharging and vanderwaals)
neturalize MMB4
&cntrl
ntr=0, nstlim = 20000,
ntave = 1000, nscm = 10000,
ntx =7, irest =1, ntpr = 1000, ntb =1,
dt =0.001, nrespa =2,
ntt =3, gamma_ln = 1.0, tempi = 300, temp0 = 300,
ntc = 2, ntf = 2, tol = 0.00001,
ntwr = 1000, ntwx =1000,
icfe = 1, clambda = 0.12923, klambda = 6
test.group (decharging)
-O -i $PBS_O_WORKDIR/MMB4_pert.mdin -p $PBS_O_WORKDIR/MMB4_wat.prmtop -c
$PBS_O_WORKDIR
/MMB4_md14.rst -o $PBS_O_WORKDIR/MMB4_pert1.mdout -inf
$PBS_O_WORKDIR/MMB4.mdinfo -x $P
BS_O_WORKDIR/MMB4_pert1.mdcrd -r $PBS_O_WORKDIR/MMB4_pert1.rst
-O -i $PBS_O_WORKDIR/MMB4_pert.mdin -p $PBS_O_WORKDIR/MMB4_decharge.prmtop
-c $PBS_O_WORKDI
R/MMB4_md14.rst -o $PBS_O_WORKDIR/MMB4_pert11.mdout -inf
$PBS_O_WORKDIR/MMB4_1.info -x
$PBS_O_WORKDIR/MMB4_pert1.mdcrd -r $PBS_O_WORKDIR/MMB4_pert1.rst
vanderwaals
-O -i $PBS_O_WORKDIR/MMB4_pert.mdin -p
$PBS_O_WORKDIR/MMB4_decharging.prmtop -c $PBS_O_WORKDIR
/MMB4_md14.rst -o $PBS_O_WORKDIR/MMB4_pert1.mdout -inf
$PBS_O_WORKDIR/MMB4.mdinfo -x $P
BS_O_WORKDIR/MMB4_pert1.mdcrd -r $PBS_O_WORKDIR/MMB4_pert1.rst
-O -i $PBS_O_WORKDIR/MMB4_pert.mdin -p
$PBS_O_WORKDIR/MMB4_vanderwaal.prmtop -c $PBS_O_WORKDI
R/MMB4_md14.rst -o $PBS_O_WORKDIR/MMB4_pert11.mdout -inf
$PBS_O_WORKDIR/MMB4_1.info -x
$PBS_O_WORKDIR/MMB4_pert1.mdcrd -r $PBS_O_WORKDIR/MMB4_pert1.rst
and the command to run the program is
mpirun -np 16 /usr/local/amber10/x86_64/bin/sander.MPI -ng 2 -groupfile
test1.group
When I am executing the program it is giving the following message
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Unit 6 Error on OPEN:
$PBS_O_WORKDIR/MMB4_pert1.mdout
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 19339 on
node Raptor-14-27.HPC.MsState.Edu exiting without calling "finalize". This
may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
Nothing is being written to the output file. I am using Amber10 for the
first time, please tell what is wrong in my procedure.
Thanks,
manikanthan
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Tue Jun 01 2010 - 12:30:05 PDT
