MD.md

MD

The MD rules use input files (or input file templates) that are located in libs/md_parameters. Consult these files for details about the parameters that are used in the MD simulations. However, every simulation that was run as part of the workflow has its own copy of these files in the workflow/data directory, with all parameters that were used in that particular simulation.

Topology generation

For details of the topology creation, see above. MD input files are generated by the following rule:

• md_build_leap: generates a leap file to be run by md_make_topology
• md_make_topology: generates the topology files for the MD simulation

Energy minimization and equilibration

Then, the following rules are run to energy minimise and equilibrate the system:

• md_em_1: energy minimisation 1
• md_em_2: energy minimisation 2
• md_em_3: energy minimisation 3
• md_eq_1: equilibration 1
• md_eq_2: equilibration 2
• md_em_eq_analysis: analysis of the energy minimisation and equilibration steps

md_em_eq_analysis uses the following rules to extract quantities of interest:

• md_readEpot : extracts the potential energy from the MD.out file
• md_readT : extracts the temperature from the MD.out file
• md_readrho : extracts the density from the MD.out file
• md_readPress : extracts the pressure from the MD.out file

cMD

The following rules are for cMD production simulations:

• md_cMD_make_param: generates the input file for the cMD production simulation
• md_cMD_prod: runs the cMD production simulation
• md_cMD_analysis: analyses the cMD production simulation

aMD

The following rules are for aMD simulations:

• md_aMD_cMD: runs a 10 ns cMD equilibration step
• md_aMD_cMD_readE: reads the energy from the cMD equilibration step
• md_aMD_make_param: generates the input file for the aMD simulation, based on the cMD equilibration step
• md_aMD_prod: runs the aMD production simulation
• md_aMD_pre_ana: extracts boosting parameters for reweighting
• md_aMD_analysis: analyses the aMD production simulation

GaMD

The following rules are for GaMD simulations:

• md_GaMD_make_param: generates the input file for the GaMD simulation
• md_GaMD_full: runs the GaMD equilibration & production simulation
• md_gaMD_pre_ana: extracts boosting parameters for reweighting
• md_GaMD_analysis: analyses the GaMD production simulation

Comparison of different MD methods

The followin rules are for comparing different MD simulations of the same compound to each other:

• md_comp_analysis: Compare simulations of different methods, but the same compound.

Different MD runs of the same compound can be compared by specifying 3 unique hashes of the MD runs in the snakemake-config file. The hashes for any parameters that were input in the samples.tsv file are stored in the samples_old.tsv file.

An overview of the entire workflow and rules is shown in the following figure: