System I/O Error: Could not open file 'mdout.mdp'

User discussions
1

GROMACS version: 2024
GROMACS modification: No

Hello!

I recently installed GROMACS on a Ubuntu virtual machine on Windows, with CUDA support. However, when I try to run simulations, I get:

maria@PCGEC14:~/simulations/ethanol_10$ gmx grompp -f npt.mdp -c npt_2.gro -p topol.top -o npt_3.tpr
:-) GROMACS - gmx grompp, 2024 (-:

Executable: /opt/gromacs-2024/bin/gmx
Data prefix: /opt/gromacs-2024
Working dir: /home/maria/simulations/ethanol_10
Command line:
gmx grompp -f npt.mdp -c npt_2.gro -p topol.top -o npt_3.tpr

Ignoring obsolete mdp entry ‘ns_type’

Program: gmx grompp, version 2024
Source file: src/gromacs/utility/filestream.cpp (line 108)
Function: gmx::internal::FileStreamImpl::FileStreamImpl(const std::filesystem::__cxx11::path&, const char*)

System I/O error:
Could not open file ‘mdout.mdp’
Reason: Permission denied
(call to fopen() returned error code 13)

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html

Can someone help me solve it? My best guess is I messed something up in the installation.
Thank you very much :-)

2

It may be a permission related issue rather than a GROMACS issue. Are you working in a directory where you have writing privileges?

1 Like
3

Thanks, it worked indeed with chmod a+w! :)