Dear Users,
I am running an MD simulation on an RNA aptamer, (2.3 Ang resolution, 20
residues). Apart from the native state, i have generated 3 mutant forms of
the original crystal structure. These mutations correspond to either single
base mutations or base pair substitutions.
As i am not sure about the behaviour of these mutant forms, current
simulation time is limited to 100ns. I don't know whether extending the
simulation time will bring the system to convergence or the system will
fall apart.
My purpose is to generate a set of ensembles for analysis of
conformational differences in mutant forms. Can you please suggest what
should be done to enhance sampling. Is extending the time scale is a viable
solution(in case of above uncertainty)
I calculated RMSD for all heavy atoms. The curve was stable after 70ns,
but RMSD for the loops seemed to increase after 90ns.
Thanks
Asmita
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Received on Sat Mar 30 2013 - 09:00:03 PDT
