Called setPositions() on a Context with the wrong number of positions
hanboy315 opened this issue · 3 comments
hanboy315 commented
Reopen issue (wrong respository posted)...
Hi, I'm trying to build a small molecule cell and run espaloma-0.3.0 on them. I keep getting a position error stating,
/home/hy2120/miniconda/envs/openff/lib/python3.10/site-packages/dgl/backend/pytorch/tensor.py:352: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly. To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
assert input.numel() == input.storage().size(), "Cannot convert view " \
Traceback (most recent call last):
File "<stdin>", line 25, in <module>
File "/home/hy2120/miniconda/envs/openff/lib/python3.10/site-packages/openmm/openmm.py", line 3479, in setPositions
return _openmm.Context_setPositions(self, positions)
openmm.OpenMMException: Called setPositions() on a Context with the wrong number of positions
hanboy315 commented
The conda environment is
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
ambertools 23.3 py310he275f01_2 conda-forge
amberutils 21.0 pypi_0 pypi
annotated-types 0.5.0 pyhd8ed1ab_0 conda-forge
anyio 4.0.0 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py310h5764c6d_3 conda-forge
arpack 3.7.0 hdefa2d7_2 conda-forge
arrow 1.2.3 pyhd8ed1ab_0 conda-forge
asttokens 2.4.0 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
aws-c-auth 0.7.3 he2921ad_3 conda-forge
aws-c-cal 0.6.2 hc309b26_0 conda-forge
aws-c-common 0.9.0 hd590300_0 conda-forge
aws-c-compression 0.2.17 h4d4d85c_2 conda-forge
aws-c-event-stream 0.3.2 h2e3709c_0 conda-forge
aws-c-http 0.7.12 hc865f51_1 conda-forge
aws-c-io 0.13.32 h019f825_2 conda-forge
aws-c-mqtt 0.9.5 h3a0376c_1 conda-forge
aws-c-s3 0.3.14 h1678ad6_3 conda-forge
aws-c-sdkutils 0.1.12 h4d4d85c_1 conda-forge
aws-checksums 0.1.17 h4d4d85c_1 conda-forge
aws-crt-cpp 0.23.1 h40cdbb9_0 conda-forge
aws-sdk-cpp 1.11.156 h8bde0db_1 conda-forge
babel 2.12.1 pyhd8ed1ab_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 h0f2a231_0 conda-forge
boost 1.78.0 py310hc4a4660_4 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
brotli 1.1.0 hd590300_0 conda-forge
brotli-bin 1.1.0 hd590300_0 conda-forge
brotli-python 1.1.0 py310hc6cd4ac_0 conda-forge
bson 0.5.9 py_0 conda-forge
bzip2 1.0.8 h7b6447c_0
c-ares 1.19.1 hd590300_0 conda-forge
c-blosc2 2.10.2 hb4ffafa_0 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.1 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 h0c91306_1017 conda-forge
certifi 2023.7.22 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py310h255011f_3 conda-forge
charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.4 pyhd8ed1ab_0 conda-forge
contourpy 1.1.0 py310hd41b1e2_0 conda-forge
cudatoolkit 11.8.0 h4ba93d1_12 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
debugpy 1.7.0 py310hc6cd4ac_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dgl 0.9.1post1 py310_0 dglteam
edgembar 0.2 pypi_0 pypi
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
espaloma 0.3.1 pyhd8ed1ab_1 conda-forge
exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fftw 3.3.10 nompi_hc118613_108 conda-forge
filelock 3.12.3 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.42.1 py310h2372a71_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
glog 0.6.0 h6f12383_0 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gmpy2 2.1.2 py310h3ec546c_1 conda-forge
greenlet 2.0.2 py310hc6cd4ac_1 conda-forge
h5py 3.9.0 nompi_py310hcca72df_101 conda-forge
hdf4 4.2.15 h501b40f_6 conda-forge
hdf5 1.14.1 nompi_h4f84152_100 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
importlib_resources 6.0.1 pyhd8ed1ab_0 conda-forge
ipykernel 6.25.2 pyh2140261_0 conda-forge
ipython 8.15.0 pyh0d859eb_0 conda-forge
ipywidgets 8.1.0 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.0 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
jsonschema 4.19.0 pyhd8ed1ab_1 conda-forge
jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.19.0 pyhd8ed1ab_1 conda-forge
jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge
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jupyter_events 0.7.0 pyhd8ed1ab_2 conda-forge
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jupyterlab 4.0.5 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.24.0 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.8 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py310hd41b1e2_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lcms2 2.15 haa2dc70_1 conda-forge
ld_impl_linux-64 2.38 h1181459_1
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20230125.3 cxx17_h59595ed_0 conda-forge
libaec 1.0.6 hcb278e6_1 conda-forge
libarrow 13.0.0 h1ed0495_3_cpu conda-forge
libblas 3.9.0 18_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_0 conda-forge
libbrotlidec 1.1.0 hd590300_0 conda-forge
libbrotlienc 1.1.0 hd590300_0 conda-forge
libcblas 3.9.0 18_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.2.1 hca28451_0 conda-forge
libdeflate 1.18 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.4 h6a678d5_0
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgfortran-ng 13.1.0 h69a702a_0 conda-forge
libgfortran5 13.1.0 h15d22d2_0 conda-forge
libglib 2.76.4 hebfc3b9_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libgoogle-cloud 2.12.0 h840a212_1 conda-forge
libgrpc 1.56.2 h3905398_1 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge
liblapack 3.9.0 18_linux64_openblas conda-forge
libnetcdf 4.9.2 nompi_he09a3a9_107 conda-forge
libnghttp2 1.52.0 h61bc06f_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libnuma 2.0.16 h0b41bf4_1 conda-forge
libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
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libsodium 1.0.18 h36c2ea0_1 conda-forge
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libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge
libthrift 0.19.0 h8fd135c_0 conda-forge
libtiff 4.5.1 h8b53f26_1 conda-forge
libutf8proc 2.8.0 h166bdaf_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.46.0 hd590300_0 conda-forge
libwebp-base 1.3.1 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxml2 2.11.5 h232c23b_1 conda-forge
libxslt 1.1.37 h0054252_1 conda-forge
libzip 1.10.1 h2629f0a_2 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lxml 4.9.3 py310h9b7343a_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
markupsafe 2.1.3 py310h2372a71_0 conda-forge
matplotlib-base 3.7.1 py310he60537e_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mda-xdrlib 0.2.0 pyhd8ed1ab_0 conda-forge
mdtraj 1.9.9 py310h8e08b51_0 conda-forge
mistune 3.0.1 pyhd8ed1ab_0 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
mpc 1.3.1 hfe3b2da_0 conda-forge
mpfr 4.2.0 hb012696_0 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.5 py310hdf3cbec_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.8.0 pyhd8ed1ab_0 conda-forge
nbformat 5.9.2 pyhd8ed1ab_0 conda-forge
ncurses 6.4 h6a678d5_0
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.6.1 nompi_hec59055_101 conda-forge
networkx 3.1 pyhd8ed1ab_0 conda-forge
nglview 3.0.6 pyhba93850_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
notebook 7.0.3 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
numexpr 2.8.4 py310hd91493a_101 conda-forge
numpy 1.25.2 py310ha4c1d20_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openff-amber-ff-ports 0.0.3 pyh6c4a22f_0 conda-forge
openff-forcefields 2023.08.0 pyh1a96a4e_0 conda-forge
openff-interchange 0.3.14 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.3.14 pyhd8ed1ab_0 conda-forge
openff-models 0.1.0 pyh1a96a4e_1 conda-forge
openff-toolkit 0.14.3 pyhd8ed1ab_0 conda-forge
openff-toolkit-base 0.14.3 pyhd8ed1ab_0 conda-forge
openff-units 0.2.1 pyh1a96a4e_0 conda-forge
openff-utilities 0.1.9 pyh1a96a4e_0 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openmm 8.0.0 py310h5728c26_1 conda-forge
openmmforcefields 0.11.2 pyhd8ed1ab_1 conda-forge
openssl 3.1.2 hd590300_0 conda-forge
orc 1.9.0 h385abfd_1 conda-forge
overrides 7.4.0 pyhd8ed1ab_0 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 2023.2.24 pypi_0 pypi
pandas 2.1.0 py310hcc13569_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panedr 0.7.2 pyhd8ed1ab_0 conda-forge
parmed 4.1.0 py310heca2aa9_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pbr 5.11.1 pyhd8ed1ab_0 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
pdb4amber 22.0 pypi_0 pypi
perl 5.32.1 4_hd590300_perl5 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.0.0 py310h582fbeb_0 conda-forge
pint 0.21 pyhd8ed1ab_0 conda-forge
pip 23.2.1 py310h06a4308_0
pixman 0.40.0 h36c2ea0_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
platformdirs 3.10.0 pyhd8ed1ab_0 conda-forge
plotly 5.16.1 pyhd8ed1ab_0 conda-forge
pooch 1.7.0 pyha770c72_3 conda-forge
prometheus_client 0.17.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.39 pyha770c72_0 conda-forge
prompt_toolkit 3.0.39 hd8ed1ab_0 conda-forge
psutil 5.9.5 py310h1fa729e_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge
pyarrow 13.0.0 py310hf9e7431_3_cpu conda-forge
pycairo 1.24.0 py310hda9f760_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 1.10.12 py310h2372a71_1 conda-forge
pydantic-core 2.6.3 py310hcb5633a_0 conda-forge
pyedr 0.7.2 pyhd8ed1ab_0 conda-forge
pygments 2.16.1 pyhd8ed1ab_0 conda-forge
pymsmt 22.0 pypi_0 pypi
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytables 3.8.0 py310ha028ce3_2 conda-forge
python 3.10.12 hd12c33a_0_cpython conda-forge
python-constraint 1.4.0 py_0 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.18.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.10 3_cp310 conda-forge
pytorch 2.0.0 cpu_generic_py310ha25dcb8_1 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py310h2372a71_0 conda-forge
pyzmq 25.1.1 py310h5bbb5d0_0 conda-forge
qcelemental 0.26.0 pyhd8ed1ab_0 conda-forge
qcportal 0.15.8 pyhd8ed1ab_0 conda-forge
rdkit 2023.03.3 py310h399bcf7_0 conda-forge
rdma-core 28.9 h59595ed_1 conda-forge
re2 2023.03.02 h8c504da_0 conda-forge
readline 8.2 h5eee18b_0
referencing 0.30.2 pyhd8ed1ab_0 conda-forge
reportlab 4.0.4 py310h2372a71_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.10.2 py310hcb5633a_0 conda-forge
s2n 1.3.49 h06160fa_0 conda-forge
sander 22.0 pypi_0 pypi
scipy 1.11.2 py310ha4c1d20_0 conda-forge
send2trash 1.8.2 pyh41d4057_0 conda-forge
setuptools 68.0.0 py310h06a4308_0
six 1.16.0 pyh6c4a22f_0 conda-forge
sleef 3.5.1 h9b69904_2 conda-forge
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snappy 1.1.10 h9fff704_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sqlalchemy 2.0.20 py310h2372a71_0 conda-forge
sqlite 3.41.2 h5eee18b_0
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
sympy 1.12 pypyh9d50eac_103 conda-forge
tenacity 8.2.3 pyhd8ed1ab_0 conda-forge
terminado 0.17.1 pyh41d4057_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tinydb 4.8.0 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h1ccaba5_0
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py310h2372a71_0 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
traitlets 5.9.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.7.1 hd8ed1ab_0 conda-forge
typing_extensions 4.7.1 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2023c h04d1e81_0
ucx 1.14.1 h64cca9d_4 conda-forge
unicodedata2 15.0.0 py310h5764c6d_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.0.4 pyhd8ed1ab_0 conda-forge
validators 0.22.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.6.2 pyhd8ed1ab_0 conda-forge
wheel 0.38.4 py310h06a4308_0
widgetsnbextension 4.0.8 pyhd8ed1ab_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.6 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.4.2 h5eee18b_0
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.16.2 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
hanboy315 commented
I've allowed the topology to be the same as my 'molecule'. If there is only one molecule it works (sure) but if it's >1 the problem remains. My .py now looks something like this. My workflow begins with packmol'ing two small molecules and that is the Y6_2_out.mol/.gro
import os
import torch
import espaloma as esp
from openff.toolkit.utils import get_data_file_path
from openmm.app import *
from openmm import *
from openmm.unit import *
from sys import stdout
from openff.toolkit.topology import Topology, Molecule
from openff.toolkit.utils.toolkits import RDKitToolkitWrapper
# read in molecules to molecular dynamics
startpositions = GromacsGroFile('/home/hy2120/single-y6/espaloma_on_single_y6/dimer/Y6_2_out.gro').positions
mol_filepath = get_data_file_path('/home/hy2120/single-y6/espaloma_on_single_y6/dimer/Y6_2_out.mol')
# See here: https://docs.openforcefield.org/projects/toolkit/en/stable/users/molecule_cookbook.html#from-small-molecule-pdb-file
molecule = Molecule.from_file(mol_filepath,"mol", toolkit_registry=RDKitToolkitWrapper())
molecule_graph = esp.Graph(molecule)
# load Espaloma
espaloma_model = esp.get_model("latest")
espaloma_model(molecule_graph.heterograph)
omm_system = esp.graphs.deploy.openmm_system_from_graph(molecule_graph)
# OK; we have our force-field now
# ensure we have correct Topology objects (OpenFF and OpenMM, jeese)
off_topology = Topology.from_molecules(molecule)
omm_topology = off_topology.to_openmm()
# Molecular dynamics setup
integrator = LangevinMiddleIntegrator(300 * kelvin, 1 / picosecond, 0.001 * picoseconds)
simulation = Simulation(omm_topology, omm_system, integrator)
simulation.context.setPositions(startpositions)
simulation.minimizeEnergy()
simulation.reporters.append(PDBReporter('/home/hy2120/y6/output.pdb', 1000))
simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,
potentialEnergy=True, temperature=True))
simulation.step(10000)
mikemhenry commented
Dupe of #194 (I transferred the old one and @hanboy315 opened this one in the correct location, but the old issue had more conversation that I didn't want to lose while we work out the issue)