bioexcel/biobb_gromacs

biobb_gromacs's Issues

Solvate does not zip a custom .itp included in .top ¿at random?

I am setting up systems to run RBFE calculations, so a protein+ligand system and a ligand-only system. In the ".top" files of both systems I include both 'ffMOL2.itp', with the atom types and vdW parameters of the ligand (incl. dummy atoms), and 'merged.itp', with merged parameters of the hybrid ligand.

However, when using the Solvate block, everything runs correctly but the output .zip file of the ligand-only system, with all the necessary files for the topology, does not include 'merged.itp', while for the protein+ligand system it is included in the .zip normally. Looking at the logs of the ligand-only solvate run, 'merged.itp' is correctly unzipped from the input .zip topology, but in the end to zip everything back it is not detected at all, not even as a file to ignore, like the ff or the water .itp. It looks like it is not detected at all by the relevant biobb_common.tools methods.

I include the input files and code (.ipynb) to reproduce.

bug.zip

Environment

$conda list
# packages in environment at /home/francho.nerin-fonz/miniforge3/envs/biobb_wf_pmx_tutorial:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_sysroot_linux-64_curr_repodata_hack 4                   h5bd9786_17    conda-forge
ambertools                23.3            py310hc095264_3    conda-forge
amberutils                21.0                     pypi_0    pypi
anyio                     4.4.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h2372a71_4    conda-forge
arpack                    3.8.0           nompi_h0baa96a_101    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
attrs                     23.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
binutils                  2.40                 h4852527_7    conda-forge
binutils_impl_linux-64    2.40                 ha1999f0_7    conda-forge
binutils_linux-64         2.40                 hb3c18ed_0    conda-forge
biobb_analysis            4.2.0              pyhdfd78af_0    bioconda
biobb_common              4.2.0              pyhdfd78af_0    bioconda
biobb_gromacs             4.2.0              pyhdfd78af_0    bioconda
biobb_pdb_tools           4.2.0              pyhdfd78af_0    bioconda
biobb_pmx                 4.2.1              pyhdfd78af_0    bioconda
biopython                 1.84            py310hc51659f_0    conda-forge
bleach                    6.1.0              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                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
brotli-python             1.1.0           py310hc6cd4ac_1    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
c-ares                    1.32.3               h4bc722e_0    conda-forge
c-compiler                1.7.0                hd590300_1    conda-forge
ca-certificates           2024.7.4             hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.18.0               hbb29018_2    conda-forge
certifi                   2024.7.4           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py310h2fee648_0    conda-forge
chardet                   5.2.0           py310hff52083_1    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.1           py310hd41b1e2_0    conda-forge
curl                      8.9.0                h18eb788_0    conda-forge
cxx-compiler              1.7.0                h00ab1b0_1    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
cython                    3.0.10          py310hc6cd4ac_0    conda-forge
debugpy                   1.8.2           py310h76e45a6_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
edgembar                  0.2                      pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
expat                     2.6.2                h59595ed_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_2    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                 4.53.1          py310h5b4e0ec_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
gcc                       12.4.0               h236703b_0    conda-forge
gcc_impl_linux-64         12.4.0               hb2e57f8_0    conda-forge
gcc_linux-64              12.4.0               h6b7512a_0    conda-forge
greenlet                  3.0.3           py310hc6cd4ac_0    conda-forge
gromacs                   2022.2          nompi_hca75aac_100    conda-forge
gxx                       12.4.0               h236703b_0    conda-forge
gxx_impl_linux-64         12.4.0               h557a472_0    conda-forge
gxx_linux-64              12.4.0               h8489865_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hdf4                      4.2.15               h2a13503_7    conda-forge
hdf5                      1.14.3          nompi_hdf9ad27_105    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.7                pyhd8ed1ab_0    conda-forge
importlib-metadata        8.2.0              pyha770c72_0    conda-forge
importlib-resources       6.4.0              pyhd8ed1ab_0    conda-forge
importlib_metadata        8.2.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.18.1             pyh707e725_3    conda-forge
ipywidgets                8.1.3              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.25             pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0           py310hff52083_0    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_0    conda-forge
jupyter                   1.0.0             pyhd8ed1ab_10    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge
jupyter_console           6.6.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py310hff52083_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.2             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.2.4              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.11             pyhd8ed1ab_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_17    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py310hd41b1e2_1    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.1.3                h59595ed_0    conda-forge
libblas                   3.9.0           23_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcblas                  3.9.0           23_linux64_openblas    conda-forge
libcurl                   8.9.0                hdb1bdb2_0    conda-forge
libdeflate                1.20                 hd590300_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     12.4.0             ha4f9413_100    conda-forge
libgcc-ng                 14.1.0               h77fa898_0    conda-forge
libgfortran-ng            14.1.0               h69a702a_0    conda-forge
libgfortran5              14.1.0               hc5f4f2c_0    conda-forge
libglib                   2.80.3               h8a4344b_1    conda-forge
libgomp                   14.1.0               h77fa898_0    conda-forge
libhwloc                  2.8.0                h32351e8_1    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           23_linux64_openblas    conda-forge
libnetcdf                 4.9.2           nompi_h135f659_114    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.27          pthreads_hac2b453_1    conda-forge
libpng                    1.6.43               h2797004_0    conda-forge
libsanitizer              12.4.0               h46f95d5_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-devel_linux-64  12.4.0             ha4f9413_100    conda-forge
libstdcxx-ng              14.1.0               hc0a3c3a_0    conda-forge
libtiff                   4.6.0                h1dd3fc0_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.4.0                hd590300_0    conda-forge
libxcb                    1.16                 hd590300_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.7               h4c95cb1_3    conda-forge
libzip                    1.10.1               h2629f0a_3    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
markupsafe                2.1.5           py310h2372a71_0    conda-forge
matplotlib-base           3.9.1           py310h0b1de36_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert                 7.16.4               hd8ed1ab_1    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbconvert-pandoc          7.16.4               hd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  h59595ed_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.1           nompi_h228c76a_104    conda-forge
notebook                  7.2.1              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
numpy                     1.26.4          py310hb13e2d6_0    conda-forge
ocl-icd                   2.3.2                hd590300_1    conda-forge
openjpeg                  2.5.2                h488ebb8_0    conda-forge
openssl                   3.3.1                h4bc722e_2    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
packmol                   20.15.0              hc8b2c43_0    conda-forge
packmol-memgen            2023.2.24                pypi_0    pypi
pandas                    2.2.2           py310hf9f9076_1    conda-forge
pandoc                    3.3                  ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parmed                    4.2.2           py310hc6cd4ac_1    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pcre2                     10.44                h0f59acf_0    conda-forge
pdb-tools                 2.5.0              pyhd8ed1ab_0    conda-forge
pdb4amber                 22.0                     pypi_0    pypi
perl                      5.32.1          7_hd590300_perl5    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.4.0          py310hebfe307_0    conda-forge
pip                       24.1.2             pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge
plotly                    5.23.0             pyhd8ed1ab_0    conda-forge
pmx_biobb                 4.1.3           py310he3a19b2_0    bioconda
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.47             pyha770c72_0    conda-forge
prompt_toolkit            3.0.47               hd8ed1ab_0    conda-forge
psutil                    6.0.0           py310hc51659f_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_0    conda-forge
pycairo                   1.26.1          py310he029307_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pymsmt                    22.0                     pypi_0    pypi
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.14         hd12c33a_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    4_cp310    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py310h2372a71_1    conda-forge
pyzmq                     26.0.3          py310h6883aea_0    conda-forge
qhull                     2020.2               h434a139_5    conda-forge
qtconsole-base            5.5.2              pyha770c72_0    conda-forge
qtpy                      2.4.1              pyhd8ed1ab_0    conda-forge
rdkit                     2023.03.3       py310h399bcf7_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
reportlab                 4.2.2           py310hc51659f_0    conda-forge
requests                  2.32.3             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                   0.19.1          py310h42e942d_0    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.13.1          py310h93e2701_0    conda-forge
send2trash                1.8.3              pyh0d859eb_0    conda-forge
setuptools                71.0.4             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.2.1                ha2e4443_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sqlalchemy                2.0.31          py310hc51659f_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
sysroot_linux-64          2.12                he073ed8_17    conda-forge
tenacity                  9.0.0              pyhd8ed1ab_0    conda-forge
terminado                 0.18.1             pyh0d859eb_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4.1           py310hc51659f_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
unicodedata2              15.1.0          py310h2372a71_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.2              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.6.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.11             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               1.8.9                hb711507_1    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                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.5                h75354e8_4    conda-forge
zipp                      3.19.2             pyhd8ed1ab_0    conda-forge
zlib                      1.3.1                h4ab18f5_1    conda-forge
zstandard                 0.23.0          py310h64cae3c_0    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

gmxselect biobb does not pass docker test

genrestr bb, possibility to add the new position restraint file in the topology (avoiding overwrite)

gmx genrestr bb is now typically used to overwrite an already existing position restraint file, because it is already included in the GROMACS topology file as ifdef. Example:

; Include Position restraint file
#ifdef POSRES
#include "posre_Protein_chain_C.itp"
#endif

Could we explore the possibility to have a new bb or an extension of this one, able to modify the topology with the new protein restraint itp files inside?

gmx_select does not run in docker

Hi Dough,

This is an example of a Docker call of Gmx Select using a selection with two named groups (“Mynewgroup” and "Protein-H”). It has been tested without success in the Gromacs docker images 2018.4 and 2020.2

docker run -v $(pwd):/inout gromacs/gromacs:latest /bin/bash -c "gmx -nobackup -nocopyright select -s /inout/make_ndx.tpr -on /inout/output_ndx.ndx -select ' "Mynewgroup" group "Protein-H" and not same residue as within 0.4 of resname ARG\’ "

Regards,
Pau Andrio

<make_ndx.tpr>

Solvate create new selection property for the solvent

if input_solvent_gro_path file is not used, check the solvent property where the gromacs defaults can be selected

new grompp/mdrun behaviour conflicts with .cpt file?

Hi,
I've recently updated to 3.9 and it seems that now everything is run inside a temporary sandbox dir while previously only the .zip topology file was decompressed inside a temporary folder.

So now, if I want to restart a run from a checkpoint file I get this error:

Program:     gmx mdrun, version 2022
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 192)
Function:    void gmx::{anonymous}::throwBecauseOfMissingOutputFiles(const char*, gmx::ArrayRef<const gmx_file_position_t>, int, const t_filenm*, size_t)

Inconsistency in user input:
Some output files listed in the checkpoint file
/home/pbarletta/labo/22/locuaz/e458d803-2586-4812-adfa-810796b54b4b/npt_nb.cpt
are not present or not named as the output files by the current program:)
Expected output files that are present:

Expected output files that are not present or named differently:

/home/pbarletta/labo/22/locuaz/faf79796-f8fe-4f8b-8647-2bd6f6d90226/npt_nb.log

/home/pbarletta/labo/22/locuaz/faf79796-f8fe-4f8b-8647-2bd6f6d90226/npt_nb.xtc

/home/pbarletta/labo/22/locuaz/faf79796-f8fe-4f8b-8647-2bd6f6d90226/npt_nb.edr

That is, since the temporary dir (faf79796-f8fe-4f8b-8647-2bd6f6d90226) always changes, I can't properly restart an MD.

Am I getting this right or is there something else going on? Because this would be quite an issue for most workflows, I assume.

New tool: gmx insert-molecules

Please try to integrate the gmx insert-molecules tool, to be able to generate Mixed Solvent MD boxes.

gmx select, append new generated group to input ndx

gmx_select has an optional input named input_ndx_path. The functionality of this bb is exactly the one of the GROMACS select tool: it produces a new index file (ndx) with (only) the newly generated group. It would be really good if the output ndx file could contain not only the new group, but all the groups defined in the input ndx file + the new group (append).

grompp_mdrun: Recover intermediate .tpr as output?

gmx make_ndx string mask

In biobb_gromacs.make_ndx, the string mask (e.g. echo -e 'a D*\n0 & ! 19\nname 20 FREEZE\nq') is not properly read.

Testing the same tutorial in version 3.6 / 3.7 (with biobb_md instead of biobb_gromacs) runs properly.

Can be something related with the new biobb_common?

genion concentration default

The concentration property, should have 0 as default value instead of 0.05.

Change pre-configured mdp files

Pre-configured mdp files in the gromacs.grompp and gromacs.grompp_mdrun building blocks should be changed by the official GROMACS mdp files from the official MD setup tutorial:
https://gitlab.com/gromacs/online-tutorials/md-intro-tutorial/-/tree/main/data/input

install error

Hi,

I'm trying to conda install and I get the following error:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.35=0
  - feature:|@/linux-64::__glibc==2.35=0

Your installed version is: 2.35

My os is Ubuntu 22.04.1

I've already got biobb_common installed.

Also, does this try to conda install gromacs? Can I use my own existing install?

Thank you,
Dan

gmx genion input ndx + enable group selection

gmx genion bb needs a new optional input: input_ndx_path, to be able to use custom groups where to add the ions (e.g. second water shell). Besides, a new property should be included, enabling group selection (now hardcoded to SOL).

Update GROMACS version

Currently the las GROMACS version for MacOS is 2019.1 and the last version for linux 2020.4. So we decided to stay in 2019.1 in both for now.

We should check with the GROMACS/conda team when the conda package for MacOS will be updated.

Default mdp files from the official gromacs tutorials

grompp (and grompp + mdrun) wrapper/s should use the official mdp files from the gromacs tutorials:
https://gitlab.com/gromacs/online-tutorials/md-intro-tutorial/-/tree/main/data/input

They have separated mdp files for amber and charmm, min, nvt, npt and md (free).

mdrun crashes with GPU settings on a machine with GPU

Hello,

I am trying to run MD using the quay.io/biocontainers/biobb_md:3.7.2--pyhdfd78af_0 docker with GPU settings on a machine with 4 GPUS, but it crashes with the following error:

Fatal error:
Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.

I would be grateful for any insight you can provide.

Thank you,
Nazanin

Making editconf's -d flag optional

Hi!
I find myself needing the -box option on editconf*, but given that the -d flag is not optional, my -box dimensions get overwritten by it, even if I set -d to 0 or a negative value.

So, would it be possible to remove the default value here, and instead of adding it eagerly here just add something like:

if self.distance_to_molecule:
            self.cmd.append("-d " + str(self.distance_to_molecule))
            fu.log("Distance of the box to molecule: %6.2f" % self.distance_to_molecule, self.out_log, self.global_log)

I know this would leave the door open for someone not specifying neither -d nor -box, which shouldn't be allowed, right? So, perhaps what I'm asking for is to add the -box option and make it so either one of them is set.

IDK, let me know if this makes sense, I have no problem doing this myself, it should be fairly quick.

Cheers!

*: which I'll be able to use in the next release through the new dev option (thanks!)

New tool: gromacs_extra.GenerateMDP a Biobb to generate MDP files.

In gmx_image the "output_selection" property is ignored if "center" is False

If "center" property is set to False, the "center_selection" property (by default "System") seems to be used anyway. As a consequence, "output_selection" is completely ignored and "center_selection" is used to determine which atoms should be dumped in the output trajectory. I guess this is because the groups are written in the following order in the .stdin: "center_selection" "output_selection". And if no centering is requested just one group is required and just the first one is used.

Maybe the easiest solution would be to avoid including the "center_selection" group in the .stdin whenever "center" is False. In that way the default value of "center_selection" would not mess with the output group.

• OS: Ubuntu
• Python version: 3.10.0
• BioBB version 4.0.0

grompp_mdrun is not creating "output_tpr_path"

I think grompp_mdrun is using a temporal unique folder into which "internal.tpr" is written. Instead of creating the .tpr file in the corresponding step folder. Due to this, if one needs to image the trajectory afterwards with gmx_image, the .tpr file is not found in the corresponding step folder.

mdrun wrapper trr optional

Make output_trr_path optional in mdrun. Nowadays trr is almost not used.