Re: [AMBER] steered MD with restraints on a selection

From: Pinky Mazumder <>
Date: Fri, 24 Jul 2020 21:51:46 -0500


How did you plot the Force vs extension curve?


On Mon, Jun 8, 2020 at 9:44 PM Baker, Joseph <> wrote:

> 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,
> Joe
> ------
> Joseph Baker, PhD
> Associate Professor
> Department of Chemistry
> C212 Science Complex
> The College of New Jersey
> Ewing, NJ 08628
> Phone: (609) 771-3173
> Web:
> Pronouns: he/him/his
> Chair (2020), Trenton Local Section of the ACS
> Chemistry Division Councilor (2018-2021), The Council on Undergraduate
> Research
> _______________________________________________
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Pinky, Sharmi
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Received on Fri Jul 24 2020 - 20:00:06 PDT
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