Commit c54508b1 authored by Doak, Peter W's avatar Doak, Peter W
Browse files

Titan NAMD example

parent 908fb94b
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
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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
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#!/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
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