lec4

After solvation, comes nutralization and subsequent steps leading to finding the most stable conformation for the protein, the conformation free of steric
hinderance and other unstablilizing effects.

1) Neutralization takes two steps. The command for the first step is:

			$ gmx grompp -f ions.mdp -c solve.gro -p topol.top -o ions.tpr

   Here, another Gromacs module 'grompp' is called. This acts like an assembler that consumes the solvation file 'solve.gro', processes it according to the
   specification given in the .mdp file, updates the topology file and as an output, returs a binary file with a .tpr ending. The "MDP" file extension stand for
   Molecular Dynamic Parameters.


2) The 'genion' module then takes this binary file and processes it for a nutralized environment with the protein in question:

			$ gmx genion -s ions.tpr -o ions.gro -p topol.top -pname NA -nname CL -neutral

   In this command:

   			-s ions.tpr		: '-s' specifies source file which is ions.tpr
			-o ions.gro		: '-o' as usual specifies the output file.
			-p topol.top	: '-p' specifies the toplogy file, as before.
			-pname NA		: 'pname' stands for Positive ion Name. So this option specified the +ve ions that'll be used to nutralize -ve charges on the
							   protein. It should be clear that Na+ ions are being used here.
			-nname CL		: Similarly '-nname' option specified the -ve ion which is Cl- here.
			-neutral		: This tell genion to calculate how many of the respective -ve and +ve ions might be required and add them.


3) Now comes the energy minimization step. This too, is done in same two steps. First grompp is used to convert .gro file with neutral protein and prepares the
   binary file with .tpr extension according to the .mdp file that provides all the specification:

   			$ gmx grompp -f minim.mdp -c ions.gro -p topol.top -o em.tpr

4) Then 'mdrun' module takes this binary file, which is provided without any extension and does the energy minimization:

			$ gmx mdrun -deffnm em -v

   The '-deffnm' option just specifies the default filename for all the output files. After this step em.trr, em.edr and em.log are generated.


5) Now since the energy minimization step is done, 

			$ gmx energy -f em.edr -o potential.xvg

   command produces a .xvg file which are then used to generate graphical presentation. The .xvg can be visualized using the grace graphical tool by

   			$ xmgrace potential.xvg

   Since the axis lebels aren't specified in the command line, grace will label the x-axis as 'time(ps)'. Since energy minimization is done in steps, this label
   should be changed acconrdingly.

6) This is then exported to .png format using the command:

			$ xmgrace -nxy potential.xvg -hdevice PNG -hardcopy -printfile potential.png

   Here:

   		-nxy				Specifies that there would be x and y axis.
		potential.xvg		The .xvg file.
		-hdevice			Specifies the output format.
		-hardcopy			Specifies printer friendly format.
		-printfile			Export command.
		poteintil.png		Output file name.

The protein system is now ready for equilibriation.