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

Hi,
I am Dr. Dweipayan Goswami,
Welcome to my RUclips channel "Learn at ease"
In this Video I have explained how to perform Post MD simulation assessment to determine RMSD, RMSF, H-bonds, Radius of Gyration and Energy.
For more prequels to this video, more videos are available on my playlist
• Bioinformatics-Unplugged
Tutorial, Codes and Files used in this video will be found at Github :
github.com/DweipayanG/GROMACS...
It will be better if you first see these two videos before seeing this video:
EP 10 | Protein-Ligand MD Simulation in Gromacs-A to Z | all reusable commands and files provided
• EP 10 | Protein-Ligand...
EP 11 | Post MD Simulation movie for visualization Protein-Ligand complex trajectories | Gromacs
• EP 11 | Post MD Simula...

[@mdamanatullaharman905]

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

[@bassantmoustapha8145]

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

[@Ashrafwazirkhan]

Need videos on free energy calculations gmx-mmpbsa

[@Ashrafwazirkhan]

Need videos on free energy calculations mm-mmpbsa

[@youssrafatima3671]

Ineed to calculate the boltzman energy distr on gromacs help plz

[@hnisarbiotech]

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

[@NurArshad]

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.

[@945corleone]

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

[@DweipayanG]

Yes minimization energy is different than free energy change energies (mm_pbsa / mm_gbsa)

[@drusamaraza4287]

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

[@s.maheenabdulrahman9896]

why the graphs are not coming in coloured format?

[@PritamKumar-vr8pn]

how the average RMSD value is determined

[@ShivamGupta-uj4jf]

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?

[@DweipayanG]

Thats not error, thats your result which you have to interpret..

[@ultron7045]

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?

[@DweipayanG]

Em.tpr is just the tpr file formed while performing “energy minimization” hence em, while md.tpr is formed when u perform md simulation

[@ultron7045]

Thank you for your quick response sir. I appreciate your answer but I want to know the difference between both files and which to choose when

[@PraneelSingla]

@@ultron7045 energy minimization is the first step done to prepare your protein for the md simulation. you will almost never use em.tpr for rmsd calculations. unless you are trying to understand your system or working environment, you will almost perform calculations post md simulation using md.tpr

[@NurArshad]

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

[@DweipayanG]

It wont run on mac it needs stand alone GPU , not on board like in M1

[@NurArshad]

@@DweipayanG ok thanks

[@shanzamunir7506]

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

[@DweipayanG]

Increase the md time run by makin changes in mdp file

[@shanzamunir7506]

My laptop turned off in between the simulation when i increase the time for simulation an i have to start the simulation runagain due to this

[@DweipayanG]

Change power options in your pc from settings ... Pc should not go to sleep when simulation is on

[@youssrafatima3671]

@@DweipayanG please i neeed the sasa command and boltzman energy

[@DweipayanG]

Try this command
gmx sasa -f traj.xtc -s topol.tpr -surface ‘Protein’ -output ‘Protein’ -o area.xvg -odg dgsolv.xvg

[@LotfiBOUROUGAA]

SASA command PLEASE.

[@saminagul3230]

I needd SASA commands too

[@NurArshad]

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

[@DweipayanG]

No

[@Ashrafwazirkhan]

Need videos on free energy calculations gmx-mmpbsa

[@Ashrafwazirkhan]

Need videos on free energy calculations gmx-mmpbsa