6. About the mdp files

There are some things that may be difficult to track about the mdp files. One of them is the tc-grps and how they are defined. For the protein we have:

tc-grps = PROT MEMB SOLV ION

Where SOLV (for solvent) includes the water and the ions, MEMB is the membrane and includes POPC and other lipids (if present), and SOLU (for solute) is the protein and the ligand. On the _prepare_prot_tpr() and _prepare_memb_tpr() functions from src/NEMAT/nemat.py, an index is generated and used in the grompp automatically. If you are having problems, look there :).

Again, the program assumes that the input files were generated using CHARMM-GUI. For the membrane, we have:

tc_grps = MEMB SOLV LIG

Which is as stated before, but now the ligand, since it’s the only solute, is named LIG.

The default mdp files are stored in the mdppath folder. This folder contains:

  1. Minimization files for the protein, the ligand, and the membrane systems. These are named as “prot_em_l0.mdp”.

  2. Equilibration files for the protein (6), the ligand (1), and the membrane (6) systems. These are named as “prot_eq(n)_l0.mdp” where \(n \in [1,6]\).

  3. Production files for the protein, the ligand, and the membrane systems. They are named as “prot_md_l0.mdp”.

  4. Finally, the transitions files are named as “prot_ti_l0.mdp”.

Note

If you are using your own mdp files, don’t forget to add the free energy inputs to all the mdp files. At least the init-lambda parameter is needed to indicate if the ligand is in state A or B. At the transitions, the other parameters become relevant:

; Free energy control stuff
free-energy = yes
init-lambda = 0 ; 0 for state A and 1 for state B
delta-lambda = 0
sc-alpha = 0.3
sc-sigma = 0.25
sc-power = 1
sc-coul = yes