[AMBER] steered MD with restraints on a selection

From: Baker, Joseph <bakerj.tcnj.edu>
Date: Mon, 8 Jun 2020 22:44:03 -0400

Hi all,

I am conducting some simulations where I am using the jar=1 feature in
amber18 to perform some constant velocity steered MD on some protein
filaments made of noncovalently interacting monomer subunits. I am pulling
along the central axis of the filament using fxyz=0,0,1 and place some
harmonic restraints on some atoms at the bottom of the filament. In the
pulling file I choose the two pulling groups such that one of the groups is
the same as the atoms that are restrained (to fix one end of the filament),
and the other group is at the top of the filament. That was the system
extends along the filament central axis without any significant rotation in
other directions.

For a check, I removed the restraints in one simulation, and the system
does rotate a bit, while also extending. When I compare the force output
data from both of the simulations I notice that in the simulation with
restraints on one of the two pulling groups there is a larger amount of
work recorded than in the simulation without restraints. This is presumably
because the steering which is attempting to separate those two groups is
fighting against those restraints at one end which are being used to fix
the system? While I see how this can be problematic for interpreting the
work (the effect of the restraints would have to be removed), is this
approach problematic for interpreting the force-extension curve (for
example, assigning peaks to various events that happen in the simulation,
interpreting relative sizes of force events along the elongation pathway,
etc.)? Any advice from those that have used a similar approach of steered
MD with some restraints applied would be appreciated.

Kind regards,

Joseph Baker, PhD
Associate Professor
Department of Chemistry
C212 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
Pronouns: he/him/his

Chair (2020), Trenton Local Section of the ACS
Chemistry Division Councilor (2018-2021), The Council on Undergraduate
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Received on Mon Jun 08 2020 - 20:00:02 PDT
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