Molecular dynamics simulations

Question

[Yoosef]

Hello I want to perform Molecular dynamics simulations to analyze the effect of a mutation on protein. Anybody knows the best tool and instruction for this kind of bioinformatics analyze? I want to add this analysis for the first time to my article . I will be so pleased if anyone can introduce me best software or good book or instructions.

Answer 1

[jgreener]

I have found the tutorials here for GROMACS to be very useful.

If it's your first time running MD I would recommend getting some short simulations up and running so that you make sure everything is installed correctly and you get a feel for the process. Use GPUs if you have access to them.

Once you are comfortable with the basics of MD you will want to ask the right question with it. I guess in this case you would see how the structure and dynamics of your protein changes with a mutation. MD is useful for this but you should make sure to simulate enough time to cover the timescale of the motions you are investigating - see more in this review.

[Yoosef]

Thanks a lot for your guidance . Yes, it is my first time to run this analysis for novel mutation . Hope i can learn it completely by myself. also, do you know any other source like you tube videos which can help to learn this software?