Couldn't open DCD file

From: Hazard, E. Starr (
Date: Wed Oct 31 2018 - 14:19:30 CDT

I'm not able to get this BPTI example to execute

The first error is that the program cannot open a file that does exist

ls -ltr *dcd*
-rw-r--r-- 1 hazards hazards 13512 Oct 31 15:11 bpti.dcd
-rw-r--r-- 1 hazards hazards 39984 Oct 31 15:11 bpti.dcd.BAK

If this is a permissions issue how can set permissions in a submit script?

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Couldn't open DCD file output/bpti.dcd: File exists

Here's my namd conf file

cat bpti.namd
# NAMD configuration file for BPTI
# molecular system
structure output/bpti.psf
# force field
paratypecharmm on
parameters toppar/par_all36m_prot.prm
parameters toppar/toppar_water_ions.str
parameters toppar/par_all36_lipid.prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_cgenff.prm
parameters toppar/par_all36_na.prm
exclude scaled1-4
1-4scaling 1.0
# approximations
switching on
switchdist 8
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
timestep 1.0
outputenergies 10
outputtiming 100
binaryoutput no
# molecular system
coordinates output/bpti.pdb
outputname output/bpti
dcdfreq 1000
temperature 0
reassignFreq 1000
reassignTemp 25
reassignIncr 25
reassignHold 300
minimize 1000
run 20000

here's my LSF submission script

#BSUB -n 80
#BSUB -u
export MPICH_HOME=/shared/app/mpich2-1.41pl_intel_12_install
export HYDRA_HOST_FILE=/home/hazards/machines
export PWD=/home/hazards/NAMD/:$PWD
export PATH=/home/hazards/NAMD/toppar:$PATH
/shared/app/NAMD_Linux-x86_64-multicore/charmrun ++mpiexec $MPICH_HOME/bin/mpiexec -launcher ssh -f /home/hazards/machines -n 80 \
/shared/app/NAMD_Linux-x86_64-multicore/namd2 +p80 /home/hazards/NAMD/bpti.namd > \



This message was secured via TLS by MUSC.

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:29 CST