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External gromacs SIF image #29
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I tried aliasing the 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 |
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: For your situation, I recommend two methods to solve your problem: Method 1: Method 2: 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 |
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
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