Hi all,
I am currently doing Hamiltonian replica exchange MD simulations. Now
that I want to analyze the data using MBAR, I need potential energy
information of all the replicas evaluated with all the different prmtop
files. According to the AMBER 21 manual, I can do this kind of
post-processing by performing a 1-step minimization (maxcyc=1) of my
trajectory with imin=5. However, when I compare the obtained energies
with the output in the mdout file, I am always a little off, up to a a
couple hundreds kcal/mol in either direction, even after additionally
setting ntp and/or ntc values in the input file.
So my question is now: Does AMBER actually perform 1 step of
minimization before giving out the energy values or might there be
another reason for the deviation?
Thank you very much in advance and best regards,
Richard
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Received on Fri Oct 15 2021 - 02:30:02 PDT
