In this folder, you will find all the items you need to reproduce our EVB simulations and MD simulations.


For the EVB simulations: 

You should first be familiar with the EVB method, a good starting point for this can be found here:
https://onlinelibrary.wiley.com/doi/book/10.1002/9781119245544

Each subfolder contains example input files needed to run the EVB equil and production simulations for a given system.
Further, a folder with all the coordinate files (Starting PDBs), as well as a folder with all the topology files (Topopogies) used along this work are provided.

All the required libraries and parameter files required to build the systems are provided in the folder "libs", together with the fep files for each chimera's hydrolysis step of the catalytic reaction.

Finally, the most representative structure obtained by clustering each chimera's hydrolysis step at the RS, TS and PS are provided in the folder "Clustered_Snapshots".

### 1. Equilibration part.
Example input files for the equilibration are attached alongside all the topologies and coordinate files.
Note that for each replica you need to choose a new random seed (defined in: "1.dyn_min_wat_noshake.inp")

The order of operations for the equil files is as follows:
"1.dyn_min_wat_noshake" "2.dyn_min_wat" "3.dyn_min_wat_eq" "4.dyn_min_wat_eq2" "5.dyn_cool" "6.dyn_min" "7.dyn_warm30k" "8.dyn_warm150k" "9.dyn_warm300k" "10.dyn_eq300k_1" "11.dyn_eq300k_2" "12.dyn_eq300k_3" "13.dyn_eq300k_4" "14.dyn_eq300k_5" "15.dyn_eq300k_6"

### 2. Production part.
The production runs were performed inside each equilibration run folder.
The order of the operations for the production files is sequentially.
"fep_000_*.inp", "fep_001_*.inp" "fep_{003..050}*.inp".

Note that only changing parameters are included in the fep files, parameters that don’t change between states are included in the SI tables, and can be found in qoplsaa.prm




For the MD simulations: 

1. StartingStructures
    - Structures used for all simulations in AmberMD format.
    
2. ParameterFilesWithExample
    - An Example tleap.in script to run with tleap (Ambertools) alongside the custom parameter files you would need to simulate the phosphylrated cystiene residue (CSP).
    Ran with: tleap -f tleap.in > tleap.out
    
3. MDSimulationInputFiles
    - Input files used (same for all systems) to run simulations with AmberMD. 
    - Order of operations is as follows:
        - minsolv.in 
        - mdsolv.in 
        - min.in
        - heat.in 
        - npt1.in 
        - npt2.in
        - npt3.in
        - npt4.in
        - eqnpt.in

After completion of the above protocol, production MD simulations can be performed. The file prod1.in provides an example of how to do this. 



