+ env
+ sort
}
AMBERHOME=/work/msaha/Amber18/amber18
AMBER_PREFIX=/work/msaha/Amber18/amber18
AWK=/usr/bin/awk
BASH=/bin/bash
BASH_FUNC_module()=() {  eval `/cm/local/apps/environment-modules/3.2.10/Modules/$MODULE_VERSION/bin/modulecmd sh $*`
CAT=/bin/cat
CDLMD_LICENSE_FILE=1999@login001
_CE_CONDA=
_CE_M=
CONDA_DEFAULT_ENV=westpa-2020.02
CONDA_EXE=/work/apps/python3/anaconda3/2020.02/bin/conda
CONDA_PREFIX_1=/work/apps/python3/anaconda3/2020.02
CONDA_PREFIX=/home/msaha/.conda/envs/westpa-2020.02
CONDA_PROMPT_MODIFIER=(westpa-2020.02) 
CONDA_PYTHON_EXE=/work/apps/python3/anaconda3/2020.02/bin/python
CONDA_SHLVL=2
CPATH=/cm/shared/apps/slurm/16.05.8/include
CP=/bin/cp
CPPTRAJ=/work/msaha/Amber18/amber18/bin/cpptraj
CUDA_VISIBLE_DEVICES=NoDevFiles
CUT=/usr/bin/cut
DATE=/bin/date
ECHO=/bin/echo
ENABLE_LMOD=0
ENVIRONMENT=BATCH
GPU_DEVICE_ORDINAL=NoDevFiles
GREP=/bin/grep
HEAD=/usr/bin/head
HISTCONTROL=ignoredups
HISTSIZE=1000
HOME=/home/msaha
HOSTNAME=node215
IFCONFIG=/bin/ifconfig
LANG=en_US.UTF-8
LD_LIBRARY_PATH=/work/msaha/Amber18/amber18/lib:/work/msaha/Amber18/amber18/lib:/work/msaha/Amber18/amber18/lib:/share/apps/gcc/4.8.5/cuda/9.2/extras/CUPTI/lib64:/share/apps/gcc/4.8.5/cuda/9.2/lib64:/work/apps/python3/anaconda3/2020.02/lib:/cm/shared/apps/slurm/16.05.8/lib64/slurm:/cm/shared/apps/slurm/16.05.8/lib64
LESSOPEN=||/usr/bin/lesspipe.sh %s
LIBRARY_PATH=/cm/shared/apps/slurm/16.05.8/lib64/slurm:/cm/shared/apps/slurm/16.05.8/lib64
_LMFILES_=/cm/shared/modulefiles/slurm/16.05.8:/cm/shared/modulefiles/python3/anaconda/2020.02:/cm/shared/modulefiles/cuda/9.2
LN=/bin/ln
LOADEDMODULES=slurm/16.05.8:python3/anaconda/2020.02:cuda/9.2
LOGNAME=msaha
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
MAIL=/var/spool/mail/msaha
MANPATH=/cm/shared/apps/slurm/16.05.8/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man:/opt/ibutils/share/man:/cm/local/apps/environment-modules/current/share/man:/cm/local/apps/environment-modules/current/share/man:/cm/local/apps/environment-modules/current/share/man
MKDIR=/bin/mkdir
MODULEPATH=/cm/local/modulefiles:/cm/shared/modulefiles
MODULESHOME=/cm/local/apps/environment-modules/3.2.10/Modules/3.2.10
MODULE_VERSION=3.2.10
MODULE_VERSION_STACK=3.2.10
NODELOC=
PASTE=/usr/bin/paste
PATH=/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/bin:/work/msaha/Amber18/amber18/bin:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/bin:/work/msaha/Amber18/amber18/bin:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/bin:/work/msaha/Amber18/amber18/bin:/share/apps/gcc/4.8.5/cuda/9.2/bin:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/bin:/home/msaha/.conda/envs/westpa-2020.02/bin:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/bin:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/bin:/share/apps/star-ccm/12.04.010-R8/STAR-View+12.04.010/bin:/share/apps/star-ccm/12.04.010-R8/STAR-CCM+12.04.010-R8/star/bin:/work/apps/python3/anaconda3/2020.02/bin:/work/apps/python3/anaconda3/2020.02/condabin:/cm/shared/apps/slurm/16.05.8/sbin:/cm/shared/apps/slurm/16.05.8/bin:/usr/local/bin:/usr/bin:/opt/ibutils/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/bin:/usr/local/sbin:/home/msaha/.local/bin:/home/msaha/bin
PERL=/usr/bin/perl
PMEMD=/work/msaha/Amber18/amber18/bin/pmemd -AllowSmallBox
PROPAGATION_DEBUG=1
PWD=/work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin
PYTHONPATH=/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/lib/blessings:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/lib/h5py:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/lib/wwmgr:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/src:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/lib/west_tools:/work/msaha/Amber18/amber18/lib/python2.7/site-packages:/work/msaha/Amber18/amber18/lib/python2.7/site-packages:/work/msaha/Amber18/amber18/lib/python2.7/site-packages
RM=/bin/rm
SANDER=/work/msaha/Amber18/amber18/bin/sander
SED=/bin/sed
SEG_DEBUG=1
SHELL=/bin/bash
SHLVL=5
SIM_NAME=left2right-0.5ps-6bin
SLURM_CHECKPOINT_IMAGE_DIR=/var/slurm/checkpoint
SLURM_CLUSTER_NAME=slurm_cluster
SLURM_CPUS_ON_NODE=28
SLURMD_NODENAME=node215
SLURM_GTIDS=0
SLURM_JOB_ACCOUNT=root
SLURM_JOB_CPUS_PER_NODE=28
SLURM_JOB_ID=10254428
SLURM_JOBID=10254428
SLURM_JOB_NAME=glycine-0.5ps-left2right-10000steps
SLURM_JOB_NODELIST=node215
SLURM_JOB_NUM_NODES=1
SLURM_JOB_PARTITION=flora-lab
SLURM_JOB_QOS=normal
SLURM_JOB_UID=1225
SLURM_JOB_USER=msaha
SLURM_LOCALID=0
SLURM_NNODES=1
SLURM_NODE_ALIASES=(null)
SLURM_NODEID=0
SLURM_NODELIST=node215
SLURM_NPROCS=28
SLURM_NTASKS=28
SLURM_NTASKS_PER_NODE=28
SLURM_PRIO_PROCESS=0
SLURM_PROCID=0
SLURM_SUBMIT_DIR=/work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin
SLURM_SUBMIT_HOST=login001
SLURM_TASK_PID=17453
SLURM_TASKS_PER_NODE=28
SLURM_TOPOLOGY_ADDR=node215
SLURM_TOPOLOGY_ADDR_PATTERN=node
SORT=/usr/bin/sort
SSH_CLIENT=129.252.24.152 61757 222
SSH_CONNECTION=129.252.24.152 61757 129.252.167.229 222
SSH_TTY=/dev/pts/52
TAR=/bin/tar
TERM=xterm
TMPDIR=/tmp
TR=/usr/bin/tr
UNIQ=/usr/bin/uniq
USE_LOCAL_SCRATCH=1
USER=msaha
_=/usr/bin/env
WEST_BIN=/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/bin
WEST_CURRENT_ITER=4862
WEST_CURRENT_SEG_DATA_REF=/work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/traj_segs/004862/000010
WEST_CURRENT_SEG_ID=10
WEST_CURRENT_SEG_INITPOINT_TYPE=SEG_INITPOINT_CONTINUES
WEST_PARENT_DATA_REF=/work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/traj_segs/004861/000011
WEST_PARENT_ID=11
WEST_PCOORD_RETURN=/tmp/tmpvd8m_jhf
WEST_PYTHONPATH=/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/lib/blessings:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/lib/h5py:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/lib/wwmgr:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/src:/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03/lib/west_tools
WEST_PYTHON=python3
WEST_RAND128=301789703074217643841608935840585840606
WEST_RAND16=59337
WEST_RAND32=3367906655
WEST_RAND64=8826418163116701710
WEST_RANDFLOAT=0.6573871790530721
WEST_ROOT=/home/msaha/.conda/envs/westpa-2020.02/westpa-2020.03
WEST_SIM_ROOT=/work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin
WM_PROCESS_INDEX=17
WM_ZMQ_MASTER_HEARTBEAT=100
WM_ZMQ_TIMEOUT_FACTOR=300
WM_ZMQ_WORKER_HEARTBEAT=100
XDG_RUNTIME_DIR=/run/user/1225
XDG_SESSION_ID=208607
ZSH=/bin/zsh
+ cd /work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin
+ mkdir -pv /work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/traj_segs/004862/000010
mkdir: created directory ‘/work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/traj_segs/004862/000010’
+ cd /work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/traj_segs/004862/000010
+ ln -sv /work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/amber_config/GLYonly-rm1.prmtop .
‘./GLYonly-rm1.prmtop’ -> ‘/work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/amber_config/GLYonly-rm1.prmtop’
+ ln -sv /work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/amber_config/qmmm.cv .
‘./qmmm.cv’ -> ‘/work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/amber_config/qmmm.cv’
+ '[' SEG_INITPOINT_CONTINUES = SEG_INITPOINT_CONTINUES ']'
+ sed s/RAND/59337/g /work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/amber_config/qmmm.in
+ ln -sv /work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/traj_segs/004861/000011/seg.rst ./parent.rst
‘./parent.rst’ -> ‘/work/msaha/westpa/adaptive-binning/glycine/left2right-0.5ps-6bin/traj_segs/004861/000011/seg.rst’
+ sander -O -i qmmm.in -p GLYonly-rm1.prmtop -c parent.rst -r seg.rst -x seg.nc -o seg.log -inf seg.nfo
++ mktemp
+ TEMP=/tmp/tmp.tLWvn3QTip
+ cat lcod.out
+ tail -2501
+ awk '{print $2}'
+ cat lcod.out
+ tail -2501
+ awk '{print $2}'
+ rm -f /tmp/tmp.tLWvn3QTip qmmm.in parent.rst seg.nfo seg.pdb GLYonly-rm1.prmtop