Simulated Tempering with fast on-the-fly weight determination. Inspired from Nguyen 2013.
This work is still ongoing, and seems to not work properly at the moment.
The goal of this project is to provide a tool to run Simulated Tempering. It implements algorithm described in N'Guyen 2013.
This work was initiated for a short Python project given in 2nd year of master deggree of bioinformatics. Please contact Athenais VAGINAY at [email protected] for all inquiries.
-
Python libraries/packages/ecosystems:
From standard :
-
To run MD : GROMACS 5.1.2
TODO : check if the code is functional with Python3
Just download the archive in and untargz it :
cd <path>
tar zxvf VAGINAY.athenais.tar.gz Each module can be tested (doctest) running the module as a script :
cd code
python <module_name>This causes the examples in the docsttrings to get executed and verified.
TODO : finish unit test
The code is not fully PEP8 compliant.
You can use pydoc outputed documentation.
html files are store in ./code/doc
/!
Not not cheat on arguments because combinations are not verified in the code.
TODO : verify arguments combination
The script should be able to recognize abbreviation of long option.
cd code
python ST-on-the-fly.py [-h] --Tmin TMIN --Tmax TMAX --Tnum TNUM
[--gro-filename GRO_FILENAME] [--top-filename
TOP_FILENAME] --nb-run NB_RUN --simu-type {md,mc}
[--st-mdp-template-filename ST_MDP_TEMPLATE_FILENAME]
--st-outname ST_OUTNAME
[--minimisation | --no-minimisation]
[--minimisation-mdp-filename MINIMISATION_MDP_FILENAME]
[--minimisation-outname MINIMISATION_OUTNAME]
[--gene-veloc-outname GENE_VELOC_OUTNAME]
--out-path OUT_PATH [--maxwarn MAXWARN]
[--clean-all] [-v[vv]]Arguments Explanation :
- -h, --help show this help message and exit
- --Tmin TMIN At which temperature (in Kelvin) begins the experiment
- --Tmax TMAX The maximal temperature (in Kelvin) during the experiment
- --Tnum TNUM Number of temperature in the given range [Tmin, Tmax]
- --gro-filename GRO_FILENAME : gro file to use for the ST experiment
- --top-filename TOP_FILENAME : topology file to use for the ST experiment
- --nb-run NB_RUN The number of molecular dynamics during the experiment :t_one-md * num-run = t_ST
- --simu-type {md,mc} type of simulation : md - Molecular Dynamics (currently the only working choice) mc - Monte Carlo (currently not working)
- --st-mdp-template-filename ST_MDP_TEMPLATE_FILENAME mdp file to use for the ST experiment
- --st-outname ST_OUTNAME template name for output of the ST experiment Should not match either minimisation-outname nor gene-veloc-outname
- --minimisation Run a minimisation before ST experiment
- --no-minimisation Do run a minimisation before ST experiment
- --minimisation-mdp-filename MINIMISATION_MDP_FILENAME mdp file to use for minimisation _ IF MINIMISATION _
- --minimisation-outname MINIMISATION_OUTNAME template name for output of minimisation Should not match either st-outname nor gene-veloc-outname _ IF MINIMISATION _
- --gene-veloc-outname GENE_VELOC_OUTNAME template name for output of velocities generation Should not match either st-outname nor minimisation-outname _ IF MINIMISATION _
- --out-path OUT_PATH Where the outputed results files should be store /!\ must finish by '/'
- --maxwarn MAXWARN The max number of warnings allowed when running MD
- --clean-all Clean gromacs outputs unecessary to plot the figures in N'Guyen 2013 /!\ Be carefull : NOT WORKING
- -v, --verbose Turn on detailed info log The level of verbosity is function of the v count
cd code
python ST-on-the-fly.py [-h] --Tmin TMIN --Tmax TMAX --Tnum TNUM
--gro-filename GRO_FILENAME --top-filename
TOP_FILENAME --nb-run NB_RUN --simu-type md
--st-mdp-template-filename ST_MDP_TEMPLATE_FILENAME
--st-outname ST_OUTNAME
[--no-minimisation]
--out-path OUT_PATH [--maxwarn MAXWARN]
[--clean-all] [-v[vv]]Working example :
cd code
python ST-on-the-fly.py \
--Tmin 1 --Tmax 5 --Tnum 1 \
--gro-filename ../data/ala10_md000.gro \
--top-filename ../data/ala10.top \
--nb-run 3 --simu-type md \
--st-mdp-template-filename ../data/md1.mdp --st-outname outst \
--out-path ../result/test-without-minimi/ --maxwarn 1 -vvvcd code
python ST-on-the-fly.py [-h] --Tmin TMIN --Tmax TMAX --Tnum TNUM
--gro-filename GRO_FILENAME --top-filename
TOP_FILENAME --nb-run NB_RUN --simu-type md
--st-mdp-template-filename ST_MDP_TEMPLATE_FILENAME
--st-outname ST_OUTNAME
--minimisation
--minimisation-mdp-filename MINIMISATION_MDP_FILENAME
--minimisation-outname MINIMISATION_OUTNAME
--gene-veloc-outname GENE_VELOC_OUTNAME
--out-path OUT_PATH [--maxwarn MAXWARN]
[--clean-all] [-v[vv]]Working example :
cd code
python ST-on-the-fly.py \
--Tmin 1 --Tmax 5 --Tnum 1 \
--gro-filename ../data/ala10_md000.gro \
--top-filename ../data/ala10.top \
--nb-run 3 --simu-type md \
--st-mdp-template-filename ../data/md1.mdp --st-outname outst \
--minimisation \
--minimisation-mdp-filename ../data/mini2.mdp --minimisation-outname miniout \
--gene-veloc-outname gene-vel \
--out-path ../result/test-with-minimi/ --maxwarn 1 -vvv
Not working
TODO
Use :
python plot.py ... TODO
- gro file
- top file
- mdp file
You can find a description of the format here
- cpt file
- edr file
- gro file
- log file
- mdp file
- top file
- tpr file
- xtc file
You can find a description of the format here
- cpt file
- edr file
- gro file
- log file
- mdp file
- top file
- tpr file
- xtc file
- xvg file
You can find a description of the format here
- /.results
tab separated file with following fields :
- idx : int < - attempt index
- t_current : float - time at the begining of the run
- T_current : float - temperature of the run
- E_run : float - energy of the run
- E_T : float - updated energy for T_current
- For each temperature in provided T range : f(T)
TODO : charts
-
Probabilities of attempt given by the Metropolis Criteriion is always 0 or 1 could be because energies are to big
-
The code is vulnerable to TOCTTOU (Time Of Check to Time Of Use) Error
Communication: Simulated tempering with fast on-the-fly weight determination. Nguyen PH1, Okamoto Y, Derreumaux P. 2013