You may analyze the RMSD and the number of hydrogen bonds. But the best one is to perform umbrela sampling for Gibbs Free energy calculations using the potential of mean force.

Thank you for the reply.

You can also analyze the binding free energy using the configurations of the complex from the trajectory using 'g_mmpbsa' module. it can also be decomposed into contributions to binding free energy from each residue, and contributions from each term: electrostatics, solvation term, van der Waals, and entropy.

http://rashmikumari.github.io/g_mmpbsa/Tutorial.html

Thank you very much for the useful information

Yes, you can observe the effect of the ligand on the protein through RMSD, RMSF and radius of gyration. The change that they induce in the protein can be interpreted through the plot you obtain. 

You can observe other factors also as mentioned by Dr. André S Pimentel and Dr. Hiqmet Kamberaj

From the short description, I would suggest you want to run equilibrium MD on the bound and unbound states, then compare them. If both simulations have reached equilirium in their sampling of states, then you have meaningful differences in those states. I would suggest analyzing side chain rotameric states. If changes go beyond side chains, then backbone states can be defined using principle component analysis. It's all about the differences.

Thank you for the reply. How to interpret this RMSD graph?.

Green colour indicates RMSD of protein and violet indicates RMSD of protein-ligand complex

gmx rms, gmx rmsf, gmx gyrate. GROMACS also proposes the group modules which can be helpful in grouping atoms of the system for specific analysis for example when it comes to measuring distances.

Hello Dr xavier, how u calculated RMSD, like for Green colour indicates RMSD of protein and violet indicates RMSD of protein-ligand complex. In both cases you have done least square fitting on BAckbone and calculation of protein and PRO-LIg system respectively ?

Also I need help regarding movie making of the final trajectory after simulation..

Will b really thankful to u.

I am learning how to use gromacs for MD. I got stucked at the point of observing the effect of the ligand on the protein through RMSD, RMSF and Energy graphs. I will like to get a plot like that of Dr.S.Xavier. I need help on that.

Thanks in advance.

There is no special way how to analyze your simulation data because it depends on your needs, however here are some useful sites that seems to be very fruitful for beginners...have a look:

https://www.researchgate.net/post/After_protein_ligand_simulation_in_gromacs_how_do_we_analyze_the_simulations

https://www.researchgate.net/post/Analysis_of_MD_Simulation_results

S. Xavier

To get the figure, you need to write a script that will plot results you got from Gromacs. I will attach one I have made, so it can help. Shivani Gupta Mukhtar Idris

Response to the question of Mukhtar Idris :

RMSD, RMSF, and all other plots were calculate on gromacs simulation after mdrun, commands, given here. also refer gromacs online tutorial too.

Potential energy: gmx energy -f em.edr -o potential.xvg

temperature: gmx energy -f nvt.edr -o temperature.xvg

Pressure: gmx energy -f npt.edr -o pressure.xvg

Density: gmx energy -f npt.edr -o density.xvg

RMSD plot:

gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center

gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns

RMSD plot of crystal structure :

gmx rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns

RMSF plot:

gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf.xvg -res

H-bond plot:

gmx hbond -f md_0_1_noPBC.xtc -s md_0_1.tpr -num hbond-intra-protein.xvg

gmx hbond -f md_0_1_noPBC.xtc -s md_0_1.tpr -num hbond-protein-water.xvg

Response to the question of Shivani Gupta :

It is possible to compare the two plots (ex. RMSD-ptn/ligand; RMSD/rmsd_xtal) using xmgrace or GNU plot tools.

Example:

xmgrace energy.xvg ; xmgrace pressure.xvg etc.

for GNU plot example.

plot "presssure.xvg" u 1:2 w lines

to see overlapped view of two graphs: xmgrace or qtgrace

Data -> Import -> ASCII -> (selected specific .xvg file using folder viewer)

Create G0 reads to graph and select, click to upload the plots of RMSD, RMSD_xtal.

You will get the combined graphs.

Hope it is useful.

Rajesh

These graphs (RSMD, RSMF, and energy), how can be explained after being analyzed in the MD simulation view?