Absolute rather than relative path in scripts

[Moricant]

I've run into a problem with the cd0897b release in that in the scripts that run the simulations the path passed via the -n flag includes the full absolute path to the index.ndx file:

[ ! -f Cpd_4-Cpd_1/water/lambda0/min01/min01.tpr ] && { gmx_mpi grompp -c Cpd_4-Cpd_1/water/lambda0/min01/../fullsystem_step6_093648_30102023.pdb -r Cpd_4-Cpd_1/water/lambda0/min01/../fullsystem_step6_093648_30102023.pdb -f Cpd_4-Cpd_1/water/lambda0/min01/min01.mdp -p Cpd_4-Cpd_1/water/lambda0/min01/../fullsystem_093648_30102023.top -o Cpd_4-Cpd_1/water/lambda0/min01/min01.tpr -n /work/obarker/FEP/Aurora_A/Test_New_PyAutoFEP/Aurora_A_Lit_DFG_In/Cpd_4-Cpd_1/protein/build_system_093641_30102023/index.ndx -po Cpd_4-Cpd_1/water/lambda0/min01/min01_mdout.mdp -maxwarn 3 > Cpd_4-Cpd_1/water/lambda0/min01/min01_grompp.log 2>&1 || { echo "Failed to run command at line ${LINENO}" && exit; } }
runall_Cpd_4-Cpd_1_water.sh.txt

Obviously this isn't a problem if you are running the jobs on the same machine where prepare_dual_topology.py was run but it is a problem if running elsewhere with a different filesystem.

[Moricant]

I've gone back to look at this as I needed to specify the mcs for the current system I'm looking at, and the older version I had been using that lacked this path problem was failing with that mcs.

It only affects the input to the -n flag and running with -vvvv we can see the difference in the variables passed to assemble_shell_command:
[DEBUG] Entering assemble_shell_command(gmx_bin=gmx_mpi, arg_list=['grompp', '-c', 'GL13-GL19/water/lambda0/min01/../fullsystem_step6_103257_02082024.pdb', '-r', 'GL13-GL19/water/lambda0/min01/../fullsystem_step6_103257_02082024.pdb', '-f', 'GL13-GL19/water/lambda0/min01/min01.mdp', '-p', 'GL13-GL19/water/lambda0/min01/../fullsystem_103257_02082024.top', '-o', 'GL13-GL19/water/lambda0/min01/min01.tpr', '-n', '/tmp/tmp4t7st7c3/CDK4_Gan_Lee_20240801/GL13-GL19/protein/build_system_103247_02082024/index.ndx', '-po', 'GL13-GL19/water/lambda0/min01/min01_mdout.mdp', '-maxwarn', '3'], input_data=, output_file=GL13-GL19/water/lambda0/min01/min01_grompp.log, verbosity=4)

Looking at prepare_dual_topology.py I'm not understanding why the full path is being given for the -n flag but not the -p flag, which is similarly using os.path.join:

input_list = ["grompp", "-c", last_files_names['gro'], "-r", last_files_names['gro'], "-t", last_files_names['cpt'], "-f", new_file_names_dict['md'], "-p", os.path.join(morph_dir, md_dir, '..', topology_file), "-o", new_file_names_dict['md_tpr'], '-n', os.path.join(morph_dir, md_dir, '..', '..', index_file), '-po', new_file_names_dict['mdout_mdp'], '-maxwarn', str(gmx_maxwarn)] grompp_cmd = os_util.assemble_shell_command(gmx_path, input_list, output_file=new_file_names_dict['grompp_log'], verbosity=verbosity) grompp_cmd = '[ ! -f {} ] && {{ {} }}'.format(new_file_names_dict['md_tpr'], grompp_cmd) output_data.append(grompp_cmd)

I'm hoping @luancarvalhomartins or someone else can shed some light on why this issue is happening and how to fix it. It's possible to work around by manually editing the water and protein run scripts of course, but that gets tedious very quickly.

pdt_debug_output.txt