lec6_ext

RMSF of the backbone atoms:
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Command:

			$ gmx rmsf -s md1.tpr -f neoMd.xtc -o rmsf.xvg

Naturally, this command is almost the same as the command for RMSD. The only difference is that the module that does this is 'rmsf' and the output file is named
accordingly. The RMSF was calulated for the backbone (4) against the backbone (4).



Radius of Gyration of the protein:
----------------------------------
Command:

			$ gmx gyrate -s md1.tpr -f neoMd.xtc -o gyrate.xvg

This command too, has the similar format as that of rmsd and rmsf calculation, the module however is gyrate. During the run the option 1) Protien was selected.



Hydrogen bonding calculation:
-----------------------------
Command:

			$ gmx hbond -s md1.tpr -f neoMd.xtc -num hbNum.xvg -dist hbDist.xvg

Here,
	hbond				The module that calculates parameter related to h-bond.
	-s md1.tpr			The binary file.
	-f neoMd.xtc		The portable trajectory file.
	-num hbNum.xvg		It returns the number of H-bond between protein and non-protein molecules.
	-dist hbDist.xvg	It returns the distribution of H-bonding distande between protein and non-protein molecules.


The output of this operation are hbdist.xvg and hbnum.xvg which respectively are files recording the number and the distribution of h-bonds. The H-bonds were
calculated for the protein (1) against the non-protein (11). However, if H-bond analysis is done for protein against protein, then we will get a picture for
hydrogen bonding inside protein.

Van der Waals Parameters
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There are quite a few Van der Waals parameters and their calculation is quantum mechnical in nature. As such, they won't be discussed here.