AMBER Archive (2009)

Subject: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration

From: nicholus bhattacharjee (
Date: Thu May 28 2009 - 08:37:29 CDT

Dear all,
I am running some simulations on protein. After minimization of the molecule
I am running 100 ps equilibration run before going for production run. I
just want to that is there any criteria to know that equilibration was
adequate from rmsd curve of the equilibration run. Or I have to check all
other parameters? Another query is that (this one was suggested by another
person) is there any optimum value in rmsd difference between the starting
molecule and the final configuration generated after md? Someone said that
it should not be greater that 2 Armstrong. Is it so ?

AMBER mailing list