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1.0 dev

Open Jaysen Saw requested to merge 1.0-dev into master
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test/command
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docker create --tty --interactive --name="remd_engine_test" remd:remd_engine
docker start --attach remd_engine_test
#docker create --tty --interactive --name="remd_engine_test" remd:remd_engine
#docker start --attach remd_engine_test
docker run --tty --interactive remd:remd_engine
python3 ../scripts/launch_REMD/main.py -seq seq-cyclic_peptide_baker.txt -cyclic True -temperature "300 313 329 347 367 391 418 450" -time 10