From 1bc7b9202c09912fee9cabe64dcebddd971fe4b2 Mon Sep 17 00:00:00 2001
From: Quantao <75652473+quantaosun@users.noreply.github.com>
Date: Mon, 6 Nov 2023 23:21:10 +1100
Subject: [PATCH] OpenMM environment file

---
 OpenMM_env.yml | 362 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 362 insertions(+)
 create mode 100644 OpenMM_env.yml

diff --git a/OpenMM_env.yml b/OpenMM_env.yml
new file mode 100644
index 0000000..dc7ed87
--- /dev/null
+++ b/OpenMM_env.yml
@@ -0,0 +1,362 @@
+name: base
+channels:
+  - https://mirrors.ustc.edu.cn/anaconda/pkgs/main
+  - conda-forge
+  - https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
+  - https://mirrors.ustc.edu.cn/anaconda/pkgs/free/
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_kmp_llvm
+  - alabaster=0.7.12=pyhd3eb1b0_0
+  - alsa-lib=1.2.8=h166bdaf_0
+  - ambertools=22.0=py38h6177452_1
+  - appdirs=1.4.4=pyhd3eb1b0_0
+  - argon2-cffi=21.3.0=pyhd3eb1b0_0
+  - argon2-cffi-bindings=21.2.0=py38h7f8727e_0
+  - arpack=3.7.0=hdefa2d7_2
+  - astunparse=1.6.3=py_0
+  - attr=2.5.1=h166bdaf_1
+  - attrs=22.1.0=py38h06a4308_0
+  - backcall=0.2.0=pyhd3eb1b0_0
+  - beautifulsoup4=4.11.1=py38h06a4308_0
+  - blosc=1.21.3=h6a678d5_0
+  - boost-cpp=1.74.0=h75c5d50_8
+  - bottleneck=1.3.5=py38h7deecbd_0
+  - brotli=1.0.9=h5eee18b_7
+  - brotli-bin=1.0.9=h5eee18b_7
+  - brotlipy=0.7.0=py38h27cfd23_1003
+  - bzip2=1.0.8=h7b6447c_0
+  - c-ares=1.18.1=h7f8727e_0
+  - ca-certificates=2023.01.10=h06a4308_0
+  - cerberus=1.3.4=pyhd3eb1b0_0
+  - certifi=2022.12.7=py38h06a4308_0
+  - cffi=1.15.1=py38h5eee18b_3
+  - cftime=1.5.1.1=py38hce1f21e_0
+  - charset-normalizer=2.0.4=pyhd3eb1b0_0
+  - clusterutils=0.3.1=pyhd8ed1ab_1
+  - colorama=0.4.6=py38h06a4308_0
+  - comm=0.1.2=py38h06a4308_0
+  - conda=23.1.0=py38h06a4308_0
+  - conda-package-handling=2.0.2=py38h06a4308_0
+  - conda-package-streaming=0.7.0=py38h06a4308_0
+  - contourpy=1.0.5=py38hdb19cb5_0
+  - cryptography=38.0.4=py38h9ce1e76_0
+  - cudatoolkit=10.2.89=h8f6ccaa_8
+  - curl=7.87.0=h5eee18b_0
+  - cycler=0.11.0=pyhd3eb1b0_0
+  - cython=0.29.32=py38h6a678d5_0
+  - dbus=1.13.18=hb2f20db_0
+  - decorator=5.1.1=pyhd3eb1b0_0
+  - defusedxml=0.7.1=pyhd3eb1b0_0
+  - dill=0.3.6=py38h06a4308_0
+  - docopt=0.6.2=py38h06a4308_1
+  - docutils=0.18.1=py38h06a4308_3
+  - entrypoints=0.4=py38h06a4308_0
+  - expat=2.5.0=h27087fc_0
+  - fftw=3.3.10=nompi_hf0379b8_106
+  - flit-core=3.6.0=pyhd3eb1b0_0
+  - font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
+  - font-ttf-inconsolata=2.001=hcb22688_0
+  - font-ttf-source-code-pro=2.030=hd3eb1b0_0
+  - font-ttf-ubuntu=0.83=h8b1ccd4_0
+  - fontconfig=2.14.2=h14ed4e7_0
+  - fonts-anaconda=1=h8fa9717_0
+  - fonts-conda-ecosystem=1=hd3eb1b0_0
+  - freetype=2.12.1=h4a9f257_0
+  - gdbm=1.18=hd4cb3f1_4
+  - gettext=0.21.1=h27087fc_0
+  - giflib=5.2.1=h5eee18b_1
+  - glib=2.74.1=h6239696_1
+  - glib-tools=2.74.1=h6239696_1
+  - gst-plugins-base=1.21.3=h4243ec0_1
+  - gstreamer=1.21.3=h25f0c4b_1
+  - gstreamer-orc=0.4.33=h166bdaf_0
+  - hdf4=4.2.15=h9772cbc_5
+  - hdf5=1.12.2=nompi_h2386368_101
+  - icu=70.1=h27087fc_0
+  - idna=3.4=py38h06a4308_0
+  - imagesize=1.4.1=py38h06a4308_0
+  - importlib_resources=5.2.0=pyhd3eb1b0_1
+  - ipython_genutils=0.2.0=pyhd3eb1b0_1
+  - jack=1.9.22=h11f4161_0
+  - jax=0.3.25=py38h06a4308_0
+  - jaxlib=0.3.25=py38h6a678d5_1
+  - jedi=0.18.1=py38h06a4308_1
+  - jinja2=3.1.2=py38h06a4308_0
+  - joblib=1.1.1=py38h06a4308_0
+  - jpeg=9e=h7f8727e_0
+  - jupyter=1.0.0=py38_7
+  - jupyter_client=7.4.8=py38h06a4308_0
+  - jupyter_console=6.4.4=py38h06a4308_0
+  - jupyter_core=5.1.1=py38h06a4308_0
+  - jupyter_server=1.23.4=py38h06a4308_0
+  - jupyterlab_pygments=0.1.2=py_0
+  - jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
+  - kiwisolver=1.4.4=py38h6a678d5_0
+  - krb5=1.19.4=h568e23c_0
+  - lame=3.100=h7b6447c_0
+  - lcms2=2.12=h3be6417_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - lerc=3.0=h295c915_0
+  - libaec=1.0.6=hcb278e6_1
+  - libblas=3.9.0=15_linux64_openblas
+  - libbrotlicommon=1.0.9=h5eee18b_7
+  - libbrotlidec=1.0.9=h5eee18b_7
+  - libbrotlienc=1.0.9=h5eee18b_7
+  - libcap=2.66=ha37c62d_0
+  - libcblas=3.9.0=15_linux64_openblas
+  - libclang=15.0.7=default_had23c3d_1
+  - libclang13=15.0.7=default_h3e3d535_1
+  - libcups=2.3.3=h3e49a29_2
+  - libcurl=7.87.0=h91b91d3_0
+  - libdb=6.2.32=h6a678d5_1
+  - libdeflate=1.8=h7f8727e_5
+  - libedit=3.1.20221030=h5eee18b_0
+  - libev=4.33=h7f8727e_1
+  - libevent=2.1.10=h9b69904_4
+  - libffi=3.4.2=h6a678d5_6
+  - libflac=1.4.2=h27087fc_0
+  - libgcc-ng=12.2.0=h65d4601_19
+  - libgcrypt=1.10.1=h166bdaf_0
+  - libgfortran-ng=12.2.0=h69a702a_19
+  - libgfortran5=12.2.0=h337968e_19
+  - libglib=2.74.1=h606061b_1
+  - libgomp=12.2.0=h65d4601_19
+  - libgpg-error=1.46=h620e276_0
+  - libiconv=1.17=h166bdaf_0
+  - liblapack=3.9.0=15_linux64_openblas
+  - libllvm15=15.0.7=hadd5161_0
+  - libnetcdf=4.8.1=nompi_h21705cb_104
+  - libnghttp2=1.46.0=hce63b2e_0
+  - libogg=1.3.5=h27cfd23_1
+  - libopenblas=0.3.20=pthreads_h78a6416_0
+  - libopus=1.3.1=h7b6447c_0
+  - libpng=1.6.39=h753d276_0
+  - libpq=14.5=h72a31a5_3
+  - libsndfile=1.2.0=hb75c966_0
+  - libsodium=1.0.18=h7b6447c_0
+  - libsqlite=3.40.0=h753d276_0
+  - libssh2=1.10.0=h8f2d780_0
+  - libstdcxx-ng=12.2.0=h46fd767_19
+  - libsystemd0=252=h2a991cd_0
+  - libtiff=4.5.0=h6a678d5_1
+  - libtool=2.4.7=h27087fc_0
+  - libudev1=252=h166bdaf_0
+  - libuuid=2.32.1=h7f98852_1000
+  - libvorbis=1.3.7=h7b6447c_0
+  - libwebp=1.2.4=h11a3e52_0
+  - libwebp-base=1.2.4=h5eee18b_0
+  - libxcb=1.13=h7f98852_1004
+  - libxkbcommon=1.0.3=he3ba5ed_0
+  - libxml2=2.10.3=h7463322_0
+  - libxslt=1.1.37=h873f0b0_0
+  - libzip=1.9.2=hc869a4a_1
+  - libzlib=1.2.13=h166bdaf_4
+  - llvm-openmp=14.0.6=h9e868ea_0
+  - lxml=4.9.2=py38h215a2d7_0
+  - lz4-c=1.9.4=h6a678d5_0
+  - lzo=2.10=h7b6447c_2
+  - markupsafe=2.1.1=py38h7f8727e_0
+  - matplotlib-base=3.6.2=py38h945d387_0
+  - mdtraj=1.9.7=py38hdee7691_4
+  - mistune=0.8.4=py38h7b6447c_1000
+  - mpg123=1.31.2=hcb278e6_0
+  - mpi=1.0=mpich
+  - mpich=4.0.3=h846660c_100
+  - mpiplus=v0.0.1=pyhd8ed1ab_1003
+  - multiprocess=0.70.14=py38h06a4308_0
+  - munkres=1.1.4=py_0
+  - mysql-common=8.0.32=h14678bc_0
+  - mysql-libs=8.0.32=h54cf53e_0
+  - ncurses=6.4=h6a678d5_0
+  - netcdf-fortran=4.5.4=nompi_hc402ea5_102
+  - netcdf4=1.6.2=py38h89d13dc_0
+  - nomkl=1.0=h5ca1d4c_0
+  - nose=1.3.7=pyhd3eb1b0_1008
+  - nspr=4.35=h27087fc_0
+  - nss=3.82=he02c5a1_0
+  - numexpr=2.8.3=py38h36ff5c2_101
+  - numpydoc=1.5.0=py38h06a4308_0
+  - ocl-icd=2.3.1=h7f98852_0
+  - ocl-icd-system=1.0.0=1
+  - openmm=8.0.0=py38h83c2b03_0
+  - openmmtools=0.20.0=py38h497a2fe_1
+  - openmoltools=0.8.8=pyhd8ed1ab_1
+  - openssl=1.1.1s=h7f8727e_0
+  - opt_einsum=3.3.0=pyhd3eb1b0_1
+  - packmol=20.010=h86c2bf4_0
+  - pandas=1.5.2=py38h417a72b_0
+  - pandocfilters=1.5.0=pyhd3eb1b0_0
+  - parmed=3.4.4=py38h8dc9893_0
+  - parso=0.8.3=pyhd3eb1b0_0
+  - pcre2=10.40=hc3806b6_0
+  - pdbfixer=1.8.1=pyh6c4a22f_0
+  - perl=5.34.0=h5eee18b_2
+  - pexpect=4.8.0=pyhd3eb1b0_3
+  - pickleshare=0.7.5=pyhd3eb1b0_1003
+  - pip=22.3.1=py38h06a4308_0
+  - pkgutil-resolve-name=1.3.10=py38h06a4308_0
+  - platformdirs=2.5.2=py38h06a4308_0
+  - pluggy=1.0.0=py38h06a4308_1
+  - ply=3.11=py38_0
+  - pooch=1.4.0=pyhd3eb1b0_0
+  - prometheus_client=0.14.1=py38h06a4308_0
+  - prompt_toolkit=3.0.36=hd3eb1b0_0
+  - pthread-stubs=0.3=h0ce48e5_1
+  - ptyprocess=0.7.0=pyhd3eb1b0_2
+  - pulseaudio=16.1=h4ab2085_1
+  - pure_eval=0.2.2=pyhd3eb1b0_0
+  - pycosat=0.6.4=py38h5eee18b_0
+  - pycparser=2.21=pyhd3eb1b0_0
+  - pyopenssl=22.0.0=pyhd3eb1b0_0
+  - pyparsing=3.0.9=py38h06a4308_0
+  - pyqt=5.15.7=py38ha0d8c90_3
+  - pyqt5-sip=12.11.0=py38h8dc9893_3
+  - pysocks=1.7.1=py38h06a4308_0
+  - pytables=3.7.0=py38hf134f34_3
+  - python=3.8.16=h7a1cb2a_2
+  - python-dateutil=2.8.2=pyhd3eb1b0_0
+  - python-fastjsonschema=2.16.2=py38h06a4308_0
+  - python_abi=3.8=2_cp38
+  - pyyaml=6.0=py38h5eee18b_1
+  - pyzmq=23.2.0=py38h6a678d5_0
+  - qt-main=5.15.6=h7acdfc8_2
+  - qtconsole=5.4.0=py38h06a4308_0
+  - qtpy=2.2.0=py38h06a4308_0
+  - readline=8.2=h5eee18b_0
+  - requests=2.28.1=py38h06a4308_0
+  - ruamel.yaml=0.17.21=py38h5eee18b_0
+  - ruamel.yaml.clib=0.2.6=py38h5eee18b_1
+  - scikit-learn=1.2.0=py38h6a678d5_0
+  - scipy=1.10.0=py38h10c12cc_2
+  - seaborn=0.12.2=py38h06a4308_0
+  - send2trash=1.8.0=pyhd3eb1b0_1
+  - setuptools=65.6.3=py38h06a4308_0
+  - sip=6.7.7=py38h8dc9893_0
+  - six=1.16.0=pyhd3eb1b0_1
+  - snappy=1.1.9=h295c915_0
+  - sniffio=1.2.0=py38h06a4308_1
+  - snowballstemmer=2.2.0=pyhd3eb1b0_0
+  - soupsieve=2.3.2.post1=py38h06a4308_0
+  - sphinx=5.0.2=py38h06a4308_0
+  - sphinxcontrib-applehelp=1.0.2=pyhd3eb1b0_0
+  - sphinxcontrib-devhelp=1.0.2=pyhd3eb1b0_0
+  - sphinxcontrib-htmlhelp=2.0.0=pyhd3eb1b0_0
+  - sphinxcontrib-jsmath=1.0.1=pyhd3eb1b0_0
+  - sphinxcontrib-qthelp=1.0.3=pyhd3eb1b0_0
+  - sphinxcontrib-serializinghtml=1.1.5=pyhd3eb1b0_0
+  - sqlite=3.40.1=h5082296_0
+  - stack_data=0.2.0=pyhd3eb1b0_0
+  - threadpoolctl=2.2.0=pyh0d69192_0
+  - ties_md=1.4.1=pyhd8ed1ab_0
+  - tk=8.6.12=h1ccaba5_0
+  - toml=0.10.2=pyhd3eb1b0_0
+  - toolz=0.12.0=py38h06a4308_0
+  - tornado=6.2=py38h5eee18b_0
+  - tqdm=4.64.1=py38h06a4308_0
+  - typing-extensions=4.4.0=py38h06a4308_0
+  - typing_extensions=4.4.0=py38h06a4308_0
+  - urllib3=1.26.14=py38h06a4308_0
+  - wcwidth=0.2.5=pyhd3eb1b0_0
+  - wheel=0.37.1=pyhd3eb1b0_0
+  - xcb-util=0.4.0=h166bdaf_0
+  - xcb-util-image=0.4.0=h166bdaf_0
+  - xcb-util-keysyms=0.4.0=h166bdaf_0
+  - xcb-util-renderutil=0.3.9=h166bdaf_0
+  - xcb-util-wm=0.4.1=h166bdaf_0
+  - xorg-kbproto=1.0.7=h7f98852_1002
+  - xorg-libice=1.0.10=h7f98852_0
+  - xorg-libsm=1.2.3=hd9c2040_1000
+  - xorg-libx11=1.7.2=h7f98852_0
+  - xorg-libxau=1.0.9=h7f98852_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xorg-libxext=1.3.4=h7f98852_1
+  - xorg-libxt=1.2.1=h7f98852_2
+  - xorg-xextproto=7.3.0=h7f98852_1002
+  - xorg-xproto=7.0.31=h27cfd23_1007
+  - xz=5.2.10=h5eee18b_1
+  - yaml=0.2.5=h7b6447c_0
+  - yank=0.25.2=pyhd8ed1ab_0
+  - zeromq=4.3.4=h2531618_0
+  - zlib=1.2.13=h166bdaf_4
+  - zstandard=0.18.0=py38h5eee18b_0
+  - zstd=1.5.2=ha4553b6_0
+  - pip:
+      - absl-py==1.2.0
+      - amberlite==22.0
+      - amberutils==21.0
+      - anyio==3.6.1
+      - asttokens==2.0.7
+      - babel==2.10.3
+      - bleach==5.0.1
+      - cachetools==5.2.0
+      - debugpy==1.6.2
+      - dimod==0.12.3
+      - dwave-networkx==0.8.12
+      - executing==0.9.1
+      - fastjsonschema==2.16.1
+      - fonttools==4.34.4
+      - google-auth==2.10.0
+      - google-auth-oauthlib==0.4.6
+      - grpcio==1.47.0
+      - importlib-metadata==4.12.0
+      - importlib-resources==5.9.0
+      - ipykernel==6.15.1
+      - ipython==8.4.0
+      - ipywidgets==7.7.1
+      - json5==0.9.9
+      - jsonschema==4.9.1
+      - jupyter-client==7.3.4
+      - jupyter-core==4.11.1
+      - jupyter-server==1.18.1
+      - jupyterlab==3.4.4
+      - jupyterlab-language-pack-zh-cn==3.4.post3
+      - jupyterlab-server==2.15.0
+      - jupyterlab-widgets==1.1.1
+      - markdown==3.4.1
+      - matplotlib==3.5.2
+      - matplotlib-inline==0.1.3
+      - mmpbsa-py==16.0
+      - nbclassic==0.4.3
+      - nbclient==0.6.6
+      - nbconvert==6.5.0
+      - nbformat==5.4.0
+      - nest-asyncio==1.5.5
+      - networkx==2.8.8
+      - notebook==6.4.12
+      - notebook-shim==0.1.0
+      - numpy==1.23.1
+      - oauthlib==3.2.0
+      - packaging==21.3
+      - packmol-memgen==1.2.3rc0
+      - pdb4amber==22.0
+      - pillow==9.2.0
+      - prompt-toolkit==3.0.30
+      - protobuf==3.19.4
+      - psutil==5.9.1
+      - pyasn1==0.4.8
+      - pyasn1-modules==0.2.8
+      - pygments==2.12.0
+      - pymbar==3.0.3
+      - pyrsistent==0.18.1
+      - pytraj==2.0.6
+      - pytz==2022.1
+      - requests-oauthlib==1.3.1
+      - rsa==4.9
+      - sander==22.0
+      - stack-data==0.3.0
+      - tabulate==0.8.10
+      - tensorboard==2.9.1
+      - tensorboard-data-server==0.6.1
+      - tensorboard-plugin-wit==1.8.1
+      - terminado==0.15.0
+      - ties==20.10
+      - tinycss2==1.1.1
+      - traitlets==5.3.0
+      - webencodings==0.5.1
+      - websocket-client==1.3.3
+      - werkzeug==2.2.2
+      - widgetsnbextension==3.6.1
+      - zipp==3.8.1
+prefix: /root/miniconda3