lec5

The equilibration process consists of two steps - equilibrate with respect to temperature and with respect to pressure. Each equilibrtion is done in two steps:
	
	- First, the .gro file and the specification file (.mdp file) is used to assemble a binary .tpr file using grompp module.
	- Then, the mdrun module does the necessary equlibration.

Temperature equlibration:

1. Preparing the binary file:

				$ gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr

   grompp 				The module which will assemble the binary .trp file.
   -f nvt.mdp			-f specifies a file. Here the .mdp file - the file containing the specs, is the argument of the '-f' option.
   -c em.gro			-c option specifies the file that contains the coordination. Here, em.gro is the energy minimized file.
   -r em.gro			-r option specifies the file containing the residue information.
   -p topol.top			-p specifies the name for toplogy file. topol.top is the file that contains the updated toplogy of our protein.
   -o nvt.tpr			-o specifies the output file.


2. Equilibrating the temperature:

				$ gmx mdrun -deffnm nvt -v

   mdrun				This is the module that does the molecular dynamics simulation. This time its simulating the protein and its environment coming to the
   						same temperature as our experimental condition.
   -deffnm nvt			'-deffnm' option specifies the name for every file for this operation. The input file nvt.tpr, and the various output files.
   -v					Time specification option. This is empty here because, time isn't specified in this situation.
   

Once the protein and its environment is in the same temperature as the experiment requires, its time to bring it to the same pressure:

1. Preparing the binary file:

				$ gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr

This command is like the corresponding temperatur equlibration step before:

	- npt.mdp is the specification file that follows '-f' option.
	- nvt.gro is the temperature equilibrated .gro file that's acting as the source of coordination (for -c option) and residue information (-r option).
	- nvt.cpt is a new file that came as the argument of '-t' option. The .cpt stands for "checkpoint". This files save the entire state of previous simulation.
	- -p specifies where to write topology update and -o as usual specifies the output.


2. Equilibrating the pressure:
			
				$ gmx mdrun -deffnm npt -v

Except for the filename, this command is the same as the one before.


After equilibration, its time for the actual simulation. Parameters like how many nano-seconds are being simulated and other things have to be specified in the
respective .mdp file. Like the temperature and pressure equlibration step, this too is done in same two steps, using same two Gromacs module:

1. Preparing the binary file:

				$ gmx grompp -f md.mdp -c npt.gro -r npt.gro -t npt.cpt -p topol.top -o md1.tpr

And like before, the command is the same except for the respective input, output and the spec. file name.

2. Run the simulation:

				$ gmx mdrun -deffnm md1 -v

In the current machine (Ryzen 5 CPU, GT-710 and GT-720 GPU, 8GB RAM), it took 52min 36sec for 1 ns of simulation of a protein of 129 residues without ligand.
The protein in question is Hen Egg Lysozyme (RSCB PDB accession ID: 1aki).