I am performing 300 ns MD simulation of protein-ligand complex. The ligand remains bound to protein for 200 ns but after 200 ns it goes out. What may be the possible issues? I have tried adjusting pbc conditions (pbc -nojump), still facing the same issues. Please suggest solutions to solve the issue.
good!.If you use gromacs for MD simulation, this problem can have some reasons:
1-your box size shuld have at least 2.0 angestroms distance.(I suggest use triclinic box)
2- you energy minmization should be done correctly and I recommand you to use velocity verletfor that.
3-your nvt step shuld be 200 ps and then npt time should be at least 2 nanoseconds
4- If you server in not so powerfull in cooling and ferquncy is 2.5 GHz oe lesser, use parallel mode to have the better accuracy and percision in the results
If a ligand doesn’t stay bound during simulation, it may be due to weak binding affinity, incorrect starting pose, poor force field parameters, too short simulation time, protein binding site changes, solvent effects, or setup errors.
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