My protein is a cysteine protease of 317 aa with a single point mutation. I want to simulate the mutated structure. What should be the time length ?
That depends on what you hope to study using the simulation. But in general, yes, 20 ns is far too short to study anything useful in most systems.
That depends on what you hope to study using the simulation. But in general, yes, 20 ns is far too short to study anything useful in most systems.
Justin may you suggest the recommended time for protein ligand interaction. Suppose we want to know weather ligand is table in protein active site or not.
There is no general answer to that, either. A protein-ligand interaction may occur in a relatively rigid protein and a short time frame may be adequate, but in the case of a flexible protein or an allosteric modulator, the effects may take hundreds of ns or microseconds to observe and conclude that the results are converged. It all depends on the biology and physics of the system.
Can same .mdp scripts be used for OPLS-AA/L all atom force field and AMBER-all atom force field in GROMACS?
Cutoff settings are likely different, but this also depends on which AMBER parameter set you're using. "AMBER force field" is extremely ambiguous, and the details do vary.
There is no strict rule for the run-time. It varies system to system and you must mention what do you want to look into? There are nano-second simulations as well as mili-sec ones. But in order to get a good statistics (if some time averaged properties are calculated) you may need ~50-100 ns.
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