samuelmurail / gromacs_py Goto Github PK

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I have installed gromacs_py (using pip because conda installation could not work) on an anaconda python 3.8 environment and I get: program not found !! when trying from gromacs_py import gmx.

program not found !! Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/opt/anaconda3/lib/python3.8/site-packages/gromacs_py/gmx/__init__.py", line 11, in <module> from .topsys import TopSys File "/opt/anaconda3/lib/python3.8/site-packages/gromacs_py/gmx/topsys.py", line 38, in <module> GMX_BIN = os_command.which('gmx') File "/opt/anaconda3/lib/python3.8/site-packages/os_command_py/os_command.py", line 56, in which raise IOError("program not found :", program_list) OSError: [Errno program not found :] ('gmx',)

I got error while running "md_sys.em_2_steps(out_folder=em_folder,
no_constr_nsteps=em_step_number,
constr_nsteps=em_step_number,
posres="",
create_box_flag=False,
emtol=0.1, nstxout=100)"

Error is "Internal error (bug):
Failed to compile NBNXN kernels for GPU #NVIDIA A100-SXM4-40GB
Could not build OpenCL program, error was Unknown OpenCL error: -9999

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors"

I am using Nvidia DGX A100 GPU.

ERROR gromacs_py/test/test_FreeEner.py - ValueError: could not convert string to float: '5.1.5'
ERROR gromacs_py/test/test_FreeEner.py - ValueError: could not convert string to float: '5.1.5'
ERROR gromacs_py/test/test_GmxSys.py - ValueError: could not convert string to float: '5.1.5'
ERROR gromacs_py/test/test_GmxSys.py - ValueError: could not convert string to float: '5.1.5'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
=================================================================== 4 errors in 26.01s ===================================================================

The function gmx5.insert_mol_sys() is extremly slow, due to atom search based on distance.

Need to improve the pdb_manip atom selection based on distance.

Hi,

I started playing with gromacs_py and got the following error:

>>> md_sys.prepare_top(out_folder=os.path.join(DATA_OUT, 'prot_top'), vsite=vsite, ff='amber99sb-ildn')
pdb2pqr_cli --ff AMBER --ffout AMBER --chain --ph-calc-method=propka --with-ph=7.00 tmp_pdb2pqr.pdb 00_1Y0M.pqr
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/almeida/.local/lib/python3.8/site-packages/gromacs_py/gmx.py", line 1997, in prepare_top
    coor_in = pdb_manip.Coor(pdb_in="00_" + name + ".pqr",
TypeError: __init__() got an unexpected keyword argument 'pdb_in'

pdb_in is not declared anywhere.

Any thought?

Thanks in advance,
-Yasser