I have done a 50 nano second protein simulation using Gromacs and obtained an RMSD value greater than 3 nm. is it ok to proceed with it or is the value incorrect?
Hi Aby Jimson ,
I don't think it is a question of whether it is correct or not.
I believe it is more towards why are you conducting MD simulations and what are you looking for.
Anyways, perhaps you can share the generated plot with the community so that everyone can get a better view of your results and shed their insights.
Other than that, a brief description of the protein you are working on plus the parameters you used would come in handy as well.
You should focus on the variation of the value rather than the mean value. If the RMSD value is about 3 +- 0.1 nm, then it's okay, as the protein reached its equilibrium state and underwent small transformations. However, it still depends on your interpretation and I recommend visualizing it using VMD or pymol to make sure the protein was equilibrated.
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