[AMBER] guidance for microsecond long MD simulations

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Wed, 5 May 2021 22:40:24 +0530

Dear All,
I'm planning to run long MD simulations 500 ns to 1 us with Amber, to
understand how ligand binding affect protein dynamics and other properties
(e.g. redox).
Since I would be running such longer MD simulations for the first time.
I thought it would make sense to take some advice from the experts on the
A google search for "guidelines for long MD simulations amber" did not
return anything particularly useful. Nonetheless, please do suggest any
reviews tutorials that might be useful here.

I understand there will be variations depending on the type, size and
nature of the system and what one wants to use the simulations for.
Nonetheless, I want to know if there are some common pitfalls to watch for
and some rule of thumb/guidelines that one should consider before running
such long and very long simulations.

Following are some of the questions that come to mind, but I don't know how
to decide what would be the best choice for various systems that I might
want to study (system size ranges from 150 to 700 residues).
1) Should one break down a long 1 microsecond simulation into 5-10 runs?
what should be the choice for "ig" parameter -1 or 0? How often people run
a full 1 microsecond simulation in one job (assuming smooth power supply)?
2) How often should I save the rst7, mdout and traj files to ensure
meaningful analysis that might be possible using a large number of cpptraj
3) It is recommended in recent literature to ensure reproducibility by
performing at least 5 identical runs with (different) random seeds. This
would increase the data storage, analysis and handling requirements
significantly. Any suggestions on these aspects?
4) For some properties like ET parameters, I think over-sampling might be a
wrong thing to do, because ET events may happen on shorter time scales (ps
to a few ns and not 100s of ns or microseconds). But again here again an
ensemble of conformations most favourable to ET is not known (& difficult
to predict) thus not clear how much sampling is ideal or too much?

I'm sure there are other aspects which I'm missing here, thus requesting
users, developers and experts to suggest.
Looking forward to hearing valuable suggestions from the list.
Thank you and best regards.

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
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Received on Wed May 05 2021 - 10:30:02 PDT
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