Hi,
I'm doing MD simulation using Amber. Every time when I measure the RMSF and RMSF it is always very high. I don't know what is the problem. THe RMSD remains stable but get high as 6 to 10 Angstrom. is this a problem or not. I also extend my simulation but no fruitful results till now.
I have also attached an RMSD plot for reference.
It is not a problem, its normal behavior of protein. It is due to initial fluctuations in the structures which are stabilized as simulation goes towards end. It would be better if you check RMSD from 1st nanosecond.
@Hammad Mirza Mubeen: Thank you very much. You can see the RMSD values are too high though it goes stable and another thing is my targeted protein has a loop of approximately half of the residues.
As per my experience, higher RMSD at start is due to random movement of protein atoms in such a way to stabilize protein. As you said there is a loop in your structure, I think you should change your simulation parameters according to loop residues. You can find in AMBER manual there is a simulation named AMD, that you can use. There are some other also simulation types for loop analysis providing higher conformation search space.
RMSD has got very less interference with the stability. It only measures the convergence. The converged system can be good for further analysis like RMSF, etc., From the RMSD of yours, I don't find anything wrong. It is showing good results. But as you mentioned about loops, I would suggest you to carry out loop refinement and then proceed with dynamics studies.
Hi
First share the protein resolution and are you taking the structure from PDB?
As you mentioned your structure contain half of loop and if it's a crystal structure with good resolution, then no need to go for loop refinement. But if you are modelling the protein by homology or ab-initio then you must have to do loop refinement. You can't find anything worthy within 5ns simulation. So my suggestion is do a long equilibration and do production for long time scale (minimum 50ns) for some worthy results.
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