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dptech-corp / Uni-GBSA

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.
Apache License 2.0
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External gromacs SIF image #29

Closed mmagithub closed 1 year ago

mmagithub commented 1 year ago

Hi,

The tool seems to require a pre-compiled gromacs (gmx) to work from the container. Is it possible to provide the absolute path of an external gromacs container (as a docker or a singularity image) as a command line argument such that it can use it instead of looking locally for an installed gmx binaries,

Thanks

mmagithub commented 1 year ago

I tried aliasing the gmx: alias gmx='singularity run -B $PWD -B ~/Desktop/images_executables/ --nv /path_to_gromacs_image/gromacs.sif gmx'

but still I got this error:

ERROR:root:Not found gmx or gmx_mpi.

It does not matter if i add the line to ~/.bashrc...I still get the same error even just typing gmx into a terminal will run gromacs..it seems the gmx path is somehow hard coded

Aunity commented 1 year ago

Hi,

The Uni-GBSA need an executable gmx or gmx_mpi in the environment variable. If the executable gmx and gmx_mpi commands are not found, it will raise the error: ERROR:root:Not found gmx or gmx_mpi.

For your situation, I recommend two methods to solve your problem:

Method 1: Using the conda create -n gbsa -c conda-forge acpype openmpi mpi4py gromacs to install the dependencies required by Uni-GBSA.

Method 2: Write the command line 

singularity run -B $PWD -B /home/marawan/Desktop/images_executables/ --nv /path_to_gromacs_image/gromacs.sif gmx $@

into a file named gmx, and give this file an executable permission through chmod +x gmx. Then put the gmx file in /anywhere/path/, and add this folder to PATH by export PATH=/anywhere/path/:$PATH.