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RunningAmber18FromCottontail2WithSlurm

Heating/Equilibration/Dynamics Template (GPU)

#!/bin/bash
#SBATCH --job-name="18GPU"
#SBATCH --output=18GPU
#SBATCH --error=18GPU
#SBATCH --partition=mwgpu
#SBATCH -B 1:1:1
#SBATCH --cpus-per-gpu=1
#SBATCH -N 1

# env
export PATH=/home/apps/CENTOS7/amber/amber18/bin:$PATH
export LD_LIBRARY_PATH=/home/apps/CENTOS7/amber/amber18/lib:/home/apps/CENTOS7/amber/amber18/lib64:$LD_LIBRARY_PATH
export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH
export CUDA_HOME=/usr/local/n37-cuda-9.2
export PATH=/usr/local/n37-cuda-9.2/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/n37-cuda-9.2/lib64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH="/usr/local/n37-cuda-9.2/lib:${LD_LIBRARY_PATH}"

### AMBER18 ###
source /share/apps/CENTOS7/amber/amber18/amber.sh

###########
# MD Runs #
###########

### EXPT 1 ###

# 20ps Heating step
pmemd.cuda -O -i heat.in  -p /home66/kscopino/CODONS/GCU/TLEAP/5JUP_N2_GCU_wat.prmtop -c /home66/kscopino/CODONS/GCU/EMIN/5JUP_N2_GCU_emin11.rst -r 5JUP_N2_GCU_heat_5.rst -ref /home66/kscopino/CODONS/GCU/EMIN/5JUP_N2_GCU_emin11.rst -o 5JUP_N2_GCU_heat_5.out -x mdcrd_heat_5 -inf mdinfo_heat_5

Paths to Python Scripts

     /home66/kscopino/BIN/N2_SCRIPTS/make_heat_equil_dyn_scripts.py