EP 12 | Post MD simulation assessment of Protein Ligand Complex in Gromacs | RMSD, RMSF, H-bonds, Rg 

Thank you, your tutorial seems very useful for us,appreciate your hard work. Hobe you will make a tutorial on MM-PBSA calculation.

Thank you very much. Waiting for GROMACS Tutorial 3: umbrella sampling videos, please

Ineed to calculate the boltzman energy distr on gromacs help plz

Dear Sir, I am using WSL instead of Virtual Box. The problem comes during WSL is that softwares like grace is unable to install. I presume that WSl doesn't supports GUI based tools. Pleas tell me a solution for it

Hi, I have run an MD simulations for 100ns on protein-protein complex, and I am currently trying to analyse the results. However, while I was running the simulations, there was a power cut-off on my PC and in order to continue the simulations, I extended the running time for another 20ns. unfortunately, when I tried to generate the RMSD plot, I noticed that the plot did not start from 0ns but from around 90ns, and the value of the RMSD just shoot to around 2.9-3.0nm. I also had another simulations run for 1ns, and the graph actually starts from 0ns point. So, I actually noticed that I have few parts of the xtc files and planned to combine them so I get to generate a continuous RMSD plot from 0ns to 120ns using this command gmx trjcat -f *.xtc -o fixed.xtc but I have been getting errors. Would you suggest any advice for me? Thank you in advanced.

why the graphs are not coming in coloured format?

Sir how to increase number of steps per minute , my system is taking 500 steps per one minute and i have to go 10ns .

how the average RMSD value is determined

I used an antibody (protein) and a ligand for the simulation. In MD movie visualization my Antibody's chains (Heavy chain and Light chain) keeps part away and join throughout the simulation also ligand deviates/fluctuates a lot. How to fix this error?

Dear Teacher, Is there any difference between the energy calculations seen at 21:04 and the energies calculated using gmx_mmpbsa?

my senior used em.tpr instead of md.tpr in rmsd calculations so would that make any difference in results? if yes, then which should i choose and why?

I am getting very less frame numbers like 10 only.. What should i do to increase it

Hi, how do I enable my GPU support on mac m1?

SASA command PLEASE.

Do we use the same tutorial for protein-protein complex?