From 38ad7bb27f39c8668083127b12a88cfb3a55d19e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sergio=20P=C3=A9rez=20Conesa?= Date: Wed, 16 Mar 2022 16:38:56 +0100 Subject: [PATCH 1/2] Update README with more accurate package info. --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 44695dd..ff2e5a8 100644 --- a/README.md +++ b/README.md @@ -19,12 +19,12 @@ using [GROMACS](http://www.gromacs.org/)[[3]](#references). ## Python dependencies -+ [Python](https://python.org) 3.8 ++ [Python](https://python.org) 3.8+ + [GROMACS](http://manual.gromacs.org/) -+ [numpy](https://numpy.org/) 1.22.1 -+ [matplotlib](https://matplotlib.org/) (analysis only) -+ [slurm](https://slurm.schedmd.com/documentation.html) (optional) -+ [plumed](https://www.plumed.org/)) (optional) ++ [numpy](https://numpy.org/) ++ [slurm](https://slurm.schedmd.com/documentation.html) (soon will be optional) ++ [plumed](https://www.plumed.org/) (optional) ++ Additional packages for analysis. (optional) The package has been tested with GROMACS2020.2. For the moment, the problem only works with CPUs but it will be adapted to use GPUs in the future. From 49bd5eab84e485de4ccb9f2628b74b26516824fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sergio=20P=C3=A9rez=20Conesa?= Date: Wed, 16 Mar 2022 16:46:31 +0100 Subject: [PATCH 2/2] documenting calling grompps respecting the slurm server --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index ff2e5a8..653a8ac 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,11 @@ using [GROMACS](http://www.gromacs.org/)[[3]](#references). The package has been tested with GROMACS2020.2. For the moment, the problem only works with CPUs but it will be adapted to use GPUs in the future. The program assumes that if you are using a cluster the queuing system is slurm, but it is easily adaptable to other -systems. The program computes the string's collective variables with gromacs' pull-code or +systems. The program should find in the path a `gmx_mpi` binary to run the simulations and a non-mpi version of the program `gmx` or `gmx_seq` to run the `grompp` commands. + +**Warning**: if only `gmx_mpi` is available grompps are run with `srun -n 1 gmx_mpi grompp`. This has made in occasions the slurm server unstable and you might receive an email from your sysadim asking you to explain why you send 300 jobs of milisecond duration in the timelapse of a second. + +The program computes the string's collective variables with gromacs' pull-code or alternatively with [plumed](https://www.plumed.org/). ## Preparing the files