Titan NAMD example

TITAN/namd/apoa1/apoa1.namd

+
+cellBasisVector1     108.8612 0.0 0.0
+cellBasisVector2     0.0 108.8612 0.0
+cellBasisVector3     0.0 0.0 77.758
+cellOrigin           0.0 0.0 0.0
+
+coordinates          apoa1.pdb
+temperature          300
+seed                 74269
+
+switching            on
+switchdist           10
+cutoff               12
+pairlistdist         13.5
+margin               0
+stepspercycle        20
+
+PME                  on
+PMEGridSizeX         108
+PMEGridSizeY         108
+PMEGridSizeZ         80
+
+structure            apoa1.psf
+parameters           par_all22_prot_lipid.xplor
+parameters           par_all22_popc.xplor
+exclude              scaled1-4
+1-4scaling           1.0
+
+timestep             1.0
+fullElectFrequency   4
+
+numsteps             500
+outputtiming         20
+
+outputname           /usr/tmp/apoa1-out
+

TITAN/namd/apoa1/par_all22_popc.xplor

+ REMARKS  Additional POPC parameters guessed by Jim Phillips
+ REMARKS  FILENAME="par_all22_popc.xplor"
+
+ ANGLE  CEL1  CEL1  CTL2     48.00   124.00  ! JCP guess 3/97
+ ANGLE  CEL1  CTL2  CTL2     32.00   112.00  ! JCP guess 3/97
+ DIHEDRAL  CEL1  CEL1  CTL2  CTL2     0.5000     3     0.00 ! JCP guess 3/97
+ DIHEDRAL  HAL1  CEL1  CTL2  CTL2     0.1200     3     0.00 ! JCP guess 3/97
+ DIHEDRAL  CEL1  CEL1  CTL2  HAL      0.1200     3     0.00 ! JCP guess 3/97
+

TITAN/namd/apoa1/run_namd.sh

+#!/bin/bash
+
+#PBS -A youracct
+#PBS -N test
+#PBS -q debug
+#PBS -j oe
+#PBS -l walltime=0:30:00
+#PBS -l nodes=100
+
+module load namd/2.12
+which namd2
+
+
+export MPICH_PTL_SEND_CREDITS=-1
+export MPICH_MAX_SHORT_MSG_SIZE=8000
+export MPICH_PTL_UNEX_EVENTS=80000
+export MPICH_UNEX_BUFFER_SIZE=100M
+
+
+NPROC=$((PBS_NUM_NODES))
+
+cd $PBS_O_WORKDIR
+#0 +ppn 7 +setcpuaffinity \
+#                                +pemap 0,2,4,6,8,10,12 +commap 14 \
+
+aprun -n $NPROC -N 1 -d 8 namd2 ++ppn 7 +setcpuaffinity \
+                                +pemap 0,2,4,6,8,10,12 +commap 14 +idlepoll +devices 0 \
+                                apoa1.namd >& apoa1_test.log
\ No newline at end of file