Dear Amber community,
This is a theoretical question and probably with a simple answer but I
can't seem to understand.
What does number of interconversions (obtained through PCA or consecutive
free energy landscape) mean? I reported the representative conformations of
all deepest energy minimum visible in my FEL plot. I also mentioned that,
for example, a particular conformation on the FEL plot occurred 30% of the
simulation time.
Is this not the number of interconversions? Should I count the number of
times that particular state was visited during the simulation. So let's say
about 85 times the simulation went to that particular energy minima?
And also, how would this give an idea of convergence of the simulation?
Any advice or suggestions will be most helpful.
Thank you
--
Best wishes
Chetna
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 08 2018 - 06:30:02 PDT
