[gmx-users] The RMSD problem

[Tanping Li]

Dear all,

Another problem bothering me for the
protein(myoglobin) is the RMSD. Because it is a very
compact protein made of 7 helices, so I expect the
RMSD should be stable and low. I follow the steps EM,
PR MD and full MD. But I still find out the RMSD is
very sensitive. It converges to 0.15nm in one of the
gound state I made, but if the initial condition is a
little bit different, it converges to 0.25 sometimes.
Could I believe that 0.15nm is the correct one and
throw away the 0.25nm one? Where does this come from,
force field or something else? Thank you very much to
share your experience and view.



Best
Tanping