Dear,
I want to run a thermodynamical integration calculation. input file and
script are like this:
Initial minimisation of protein side chains and ions
&cntrl
imin=0, irest=1, ntx=5,
cut=10, ntb=2, ntr=0,
pres0=1.0, ntp=1, taup=2.0,
ntc=2, ntf=2,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=1.0,
nstlim=5000000, dt=0.001,
ntpr=5000, ntwx=5000, ntwr=50000,
icfe=1, clambda=0.0
/
#! /bin/sh
#PBS -q dq2
#PBS -N Amber12
#PBS -l nodes=1:ppn=12
##PBS -l mem=1024MB
#PBS -e mpi_amber.err2b
#PBS -o mpi_amber.log2b
#PBS -m bea
#PBS -M ycqchemical.gmail.com
export PATH=/opt/share/Python-2.7.3/bin/:$PATH
export LD_LIBRARY=/opt/share/Python-2.7.3/lib:$LD_LIBRARY
export AMBERHOME=/opt/share/amber12
source /opt/share/etc/mpich-3.0.4.intel.sh
cd /scratch/s1007018600/comp1/input/TI/0.0
pwd
date
pbs_mpirun $AMBERHOME/bin/sander.MPI -O -i ligand-md2.in -o
ligand-md2-1.out -p complex-sol.prmtop -c ligand-md1.rst -r
ligand-md2-1.rst -x ligand-md2-1.mdcrd -ref ligand-md1.rst
date
however, when I submitted my job (qsub xxx), a mistake comes out, saying:
Fatal error in PMPI_Bcast: Invalid communicator, error stack:
PMPI_Bcast(1525): MPI_Bcast(buf=0x4b2f608, count=1, MPI_INTEGER, root=0,
comm=0x0) failed
PMPI_Bcast(1466): Invalid communicator
and the outfile is like this:
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
how can I fix this?
Thx.
C.Q.
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Received on Fri Feb 28 2014 - 00:00:03 PST
