MD tutorial returns empty trajectory #199
Description
Describe the bug
When I run the tutorial "Running an MD simulation of a protein-ligand complex", the simulation runs without error, but when I try opening the simulation.xtc file with gromacs trjconv I get:
Assertion failed:
Condition: !bOK
Inconsistent results - OK status from read_first_xtc, but 0 atom coords read
Moreover, the simulation.log file is empty and the checkpoint.chk file is missing. The other expected files, instead, don't seem wrong.
Furthermore, the simulation is suspicously fast, 7 minutes of Wall-clock time on a CPU. So my suspect is that the simulationd does not actually happen, but for some reason no error gets raised.
To Reproduce
I used exactly the same code as proposed in the tutorial
Software versions
- OpenFE version 1.2.0. (but also tried with the latest 1.3.2)
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
adjusttext 1.3.0 pyhd8ed1ab_0 conda-forge
amberlite 22.0 pypi_0 pypi
ambertools 22.5 py310hd182041_0 conda-forge
amberutils 21.0 pypi_0 pypi
annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge
anyio 4.6.2.post1 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py310ha75aee5_5 conda-forge
arpack 3.7.0 hdefa2d7_2 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
atk-1.0 2.38.0 h04ea711_2 conda-forge
attrs 24.2.0 pyh71513ae_0 conda-forge
babel 2.16.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
biopython 1.84 py310hc51659f_0 conda-forge
bleach 6.2.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.6 hef167b5_0 conda-forge
boost 1.78.0 py310hcb52e73_5 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py310hf71b8c6_2 conda-forge
bson 0.5.9 py_0 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.3 hb9d3cd8_1 conda-forge
c-blosc2 2.15.2 h68e2383_0 conda-forge
ca-certificates 2024.8.30 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.5.0 pyhd8ed1ab_0 conda-forge
cairo 1.18.0 hbb29018_2 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py310h8deb56e_0 conda-forge
cftime 1.6.4 py310hf462985_1 conda-forge
chardet 5.2.0 py310hff52083_2 conda-forge
charset-normalizer 3.4.0 pyhd8ed1ab_0 conda-forge
cinnabar 0.4.1 pyhd8ed1ab_1 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
contourpy 1.3.1 py310h3788b33_0 conda-forge
cudatoolkit 11.8.0 h4ba93d1_13 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cython 3.0.11 py310h5b1441d_3 conda-forge
debugpy 1.8.9 py310hf71b8c6_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dill 0.3.9 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge
executing 2.1.0 pyhd8ed1ab_0 conda-forge
expat 2.6.4 h5888daf_0 conda-forge
fftw 3.3.10 nompi_hf1063bd_110 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 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.55.0 py310h89163eb_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gdk-pixbuf 2.42.12 hb9ae30d_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
graphviz 12.0.0 hba01fac_0 conda-forge
greenlet 3.1.1 py310hf71b8c6_0 conda-forge
griddataformats 1.0.2 pyhd8ed1ab_0 conda-forge
gsd 3.4.2 py310ha75aee5_0 conda-forge
gtk2 2.24.33 h6470451_5 conda-forge
gts 0.7.6 h977cf35_4 conda-forge
gufe 1.1.0 pyhd8ed1ab_1 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
harfbuzz 9.0.0 hfac3d4d_0 conda-forge
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.4 nompi_h2d575fe_104 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.7 pyh29332c3_1 conda-forge
httpx 0.28.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.10 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.5.0 pyha770c72_0 conda-forge
importlib_resources 6.4.5 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 8.30.0 pyh707e725_0 conda-forge
ipywidgets 8.1.5 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.2 pyhff2d567_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
json5 0.10.0 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py310hff52083_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge
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jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_0 conda-forge
jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.14.2 pyhd8ed1ab_0 conda-forge
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jupyterlab 4.2.6 pyhff2d567_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge
jupyterlab_server 2.27.3 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.13 pyhd8ed1ab_0 conda-forge
kartograf 1.0.1 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.7 py310h3788b33_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_2 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libblas 3.9.0 25_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcblas 3.9.0 25_linux64_openblas conda-forge
libcurl 8.10.1 hbbe4b11_0 conda-forge
libdeflate 1.22 hb9d3cd8_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.6.4 h5888daf_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libgfortran 14.2.0 h69a702a_1 conda-forge
libgfortran-ng 14.2.0 h69a702a_1 conda-forge
libgfortran5 14.2.0 hd5240d6_1 conda-forge
libglib 2.82.2 h2ff4ddf_0 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 25_linux64_openblas conda-forge
libllvm14 14.0.6 hcd5def8_4 conda-forge
libnetcdf 4.9.2 nompi_h2564987_115 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.28 pthreads_h94d23a6_1 conda-forge
libpng 1.6.44 hadc24fc_0 conda-forge
librsvg 2.58.4 hc0ffecb_0 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.47.0 hadc24fc_1 conda-forge
libssh2 1.11.1 hf672d98_0 conda-forge
libstdcxx 14.2.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.2.0 h4852527_1 conda-forge
libtiff 4.7.0 he137b08_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp 1.4.0 h2c329e2_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 h4c95cb1_3 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzip 1.11.2 h6991a6a_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
llvmlite 0.43.0 py310h1a6248f_1 conda-forge
lomap2 3.1.0 pyhff2d567_0 conda-forge
lxml 5.3.0 py310h6ee67d5_2 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
markupsafe 3.0.2 py310h89163eb_0 conda-forge
matplotlib-base 3.9.2 py310h68603db_2 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mda-xdrlib 0.2.0 pyhd8ed1ab_0 conda-forge
mdanalysis 2.1.0 py310h769672d_4 conda-forge
mdtraj 1.10.1 py310he1cc299_1 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
mmtf-python 1.1.3 pyhd8ed1ab_0 conda-forge
mpiplus v0.0.2 pyhd8ed1ab_0 conda-forge
mrcfile 1.5.3 pyhd8ed1ab_0 conda-forge
msgpack-python 1.1.0 py310h3788b33_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nbclient 0.10.1 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
ncurses 6.5 he02047a_1 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.6.1 nompi_ha5d1325_107 conda-forge
netcdf4 1.7.2 nompi_py310h5146f0f_100 conda-forge
networkx 3.4.2 pyh267e887_2 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 7.2.2 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge
numba 0.60.0 py310h5dc88bb_0 conda-forge
numexpr 2.10.2 py310hdb6e06b_100 conda-forge
numpy 1.26.4 py310hb13e2d6_0 conda-forge
ocl-icd 2.3.2 hb9d3cd8_2 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
opencl-headers 2024.10.24 h5888daf_0 conda-forge
openfe 1.2.0 pyhd8ed1ab_0 conda-forge
openfe-analysis 0.2.0 pyhd8ed1ab_0 conda-forge
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pango 1.54.0 h4c5309f_1 conda-forge
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patsy 1.0.1 pyhff2d567_0 conda-forge
pcre2 10.44 hba22ea6_2 conda-forge
pdb4amber 22.0 pypi_0 pypi
pdbfixer 1.9 pyh1a96a4e_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
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pillow 11.0.0 py310hfeaa1f3_0 conda-forge
pint 0.23 pyhd8ed1ab_1 conda-forge
pip 24.3.1 pyh8b19718_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_0 conda-forge
plotly 5.24.1 pyhd8ed1ab_0 conda-forge
plugcli 0.2.0 pyhd8ed1ab_0 conda-forge
pluggy 1.5.0 pyhd8ed1ab_0 conda-forge
pooch 1.8.2 pyhd8ed1ab_0 conda-forge
prometheus_client 0.21.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.48 pyha770c72_0 conda-forge
psutil 6.1.0 py310ha75aee5_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
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python-fastjsonschema 2.21.0 pyhd8ed1ab_0 conda-forge
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python_abi 3.10 5_cp310 conda-forge
pytraj 2.0.6 pypi_0 pypi
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rmsd 1.6.4 pypi_0 pypi
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sander 22.0 pypi_0 pypi
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scipy 1.14.1 py310hfcf56fc_1 conda-forge
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xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
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xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
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xz 5.2.6 h166bdaf_0 conda-forge
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