I will use molecular dynamics simulation for the refinement of more than two protein structures. Most of the research for refinement in the literature is about the docking of two proteins. So I can't decide which simulation programme is better for this. NAMD or GROMACS?
Using any of one is a personal preference and sometimes trials and errors. The main important factor here is the force field. Again this is also personal preference. As for now, you can start with Charmm36ff with either NAMD or Gromacs. Then you can move to amber14sb. Check with 10 ns of each system, and later you can extend the simulation time.
Dear Ahmet
The right direction for protein structure analysis using MD studies, you have to decide the force field which you want to choose. Because, it is the force field which uses to solve Newtonian motion of the protein. Generally, OPLS force field is best for studying proteins having sequence length shorter than 100 amino acids. For proteins larger than 100 amino acids, generally CHARMM force field produces better results. AMBER 19sb force field can also be used.
Now to use these force fields you can use different software packages including GROMACS or NAMD. DESMOND can be used exclusively for OPLS force field. While AMBER can be used for amber 19sb or other force fields.
These are several tutorial on gromacs, you can use them as reference for performing protein dynamics.
https://www.youtube.com/watch?v=90U-t31yetA
www.youtube.com/watch?v=vLKcM_loDzg
regards
Tanuj
Dear Tanuj,
Thank you so much for this informative information. I guess the only way to do better simulation is to use an effective force field regardless of simulation programmes.
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