Dear all,
I have encountered a problem regarding the RMSD value. Based on my previous comparisons with other results on the internet, an RMSD value >3A (>0,3 nm) seems like not acceptable.
I have run simulations for several samples, each lasting 10 ns, and consistently obtained similar results with RMSD values ranging from 2-5 nm (20-50 A).
Could anyone provide insight into what might be causing such high RMSD values?
Note:
I used the AMBER99SB force field (number 5).
