Closed hanboy315 closed 11 months ago
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
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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
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freetype 2.12.1 hca18f0e_1 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
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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
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jedi 0.19.0 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
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jsonpointer 2.0 py_0 conda-forge
jsonschema 4.19.0 pyhd8ed1ab_1 conda-forge
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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
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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
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libpng 1.6.39 h753d276_0 conda-forge
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libsodium 1.0.18 h36c2ea0_1 conda-forge
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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
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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
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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
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openssl 3.1.2 hd590300_0 conda-forge
orc 1.9.0 h385abfd_1 conda-forge
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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
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pbr 5.11.1 pyhd8ed1ab_0 conda-forge
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pdb4amber 22.0 pypi_0 pypi
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pip 23.2.1 py310h06a4308_0
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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
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terminado 0.17.1 pyh41d4057_0 conda-forge
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tinydb 4.8.0 pyhd8ed1ab_0 conda-forge
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tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.3.3 py310h2372a71_0 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
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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
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uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.0.4 pyhd8ed1ab_0 conda-forge
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websocket-client 1.6.2 pyhd8ed1ab_0 conda-forge
wheel 0.38.4 py310h06a4308_0
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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
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)
Dupe of https://github.com/choderalab/espaloma/issues/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)
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,