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release_notes.txt
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######################################################################
NEW IN VERSION 2.1
######################################################################
1) Derek's scripts are integrated into the MMGBSA distribution, in a directory named ./parallel_scripts/
2) Split prepare_mmgbsa_namd.csh into two parts:
- prepare_mmgbsa_common.csh is executed once before parallelization.
- prepare_mmgbsa_local.csh is executed on each node with each small trajectory.
3) setup_charmm.sh is now a bash script. It takes an array of cappings as argument instead of separate arguments.
4) vmd_selections.tcl is now created by the top script run.sh.
5) Change in calc-inter-global.inp, such that first frame uses the right cutoffs for electrostatics.
6) Adapted mmgbsa_final_results.sh (now called mmgbsa_collect_results.sh) so that it handles arbitrary number of frames per subjob.
7) Scripts can now be run on panda as well as fido
8) Added many additional error messages to stop execution if something is wrong.
======================================================================
Modification to the parallel scripts themselves
0) Scripts are now kept in the distribution, only the top script called mmgbsa_master_submit.sh will be copied to the directory where the calculation is done. In the future, an input file should contain all the system-specific things and even the mmgbsa_master_submit.sh script should be stored only in the MMGBSA distribution.
1) setenv.sh is now called only by the top script. Parameters are passed to sub-scripts as global variables. Also, setenv.csh is not used anymore. We don't make local versions of setenv.sh and only the distribution version of setenv.sh is called,
2) Several modifications to the mmgbsa_master_submit.sh, so that setup_charmm.sh prepare_mmgbsa_common.csh are performed only once on the front end, before mmgbsa_master_submit.sh is distributed to the nodes.
3) remove sub-directory ./job_directory, and move everything up one level.
4) For final results, remove sub-directory ./final_results and copy everything at the level of the working directory.
5) Renamed some of the scripts for more consistency.
6) Submission of mmgbsa_final_submit.sh (previously run_final.sh) is done with a dependency condition, such that the jobs starts only when all subjobs have finised.
======================================================================
Typical workflow for mmgbsa2.1
In the main directory, there should be an ./input subdirectory containing a PSF and a PDB file. Source the environment :
source /home/mac2109/mmgbsa/mmgbsa2.1/scripts/setenv.sh
Copy the main script locally :
cp -rp $mmgbsa_path/RUN.sh .
Edit the parameters inside the script. Then run the entire calculation with
./scripts/generate_loader_str.sh
./RUN.sh
======================================================================