Dear Jason,
Thank you. But you can see that the method described for obtaining constant
force pulling - via Amber - has been suggested by Dr. Dan Roe and Dr.
Adrian Roitberg in the Amber mail list.
On Sunday, February 23, 2014, Jason Swails <jason.swails.gmail.com> wrote:
> On Sun, Feb 23, 2014 at 12:48 PM, Ali M. Naserian-Nik <
> naseriannik.gmail.com <javascript:;>
> > wrote:
>
> > Hi Jason,
> >
> > Thank you very much for your reply. But I think for constant force
> pulling,
> >
>
> It's been some time since I've read about this, but I believe there are two
> main 'methods' for performing steered molecular dynamics: constant force
> and constant velocity. In the first, I believe that the force acting upon
> the reaction coordinate is constant in the direction you wish to steer it
> at every step. In the second, which is the one implemented here in Amber,
> the center of a restraint potential is moved with a constant velocity along
> the reaction coordinate.
>
> Both approaches are non-equilibrium and therefore must be postprocessed
> with an ensemble of work profiles to recover the free energy profile, but I
> think there may be a difference in the way you postprocess each approach
> (but maybe not?). As far as I know, there is no way to do constant force
> pulling with Amber (at least not with the nmropt restraints). Only
> constant velocity pulling is supported.
>
> I need a linear potential not a parabolic, and r1-r4 must be set to be
> > around or smaller than the final displacement (r2a-r2). Is it true? If
> yes,
> > then how I can change value of r4?
> >
>
> A linear potential does not give you a constant force -- the farther from
> the 'center' of the potential you are the higher the force acting on the
> particle. Only that force does not grow as quickly as it does with a
> harmonic restraint. [1]
>
>
> > An additional question: What is the role of r4a?
> >
>
> I believe these variables are used if you are changing the restraint
> potential with time (see the "ifvari" variable in the NMR restraint chapter
> of the manual). In general, I would not advise using this variable with
> steered MD, since steered MD itself changes the center of the potential as
> a function of time in the simulation.
>
> HTH,
> Jason
>
> [1] Actually, a linear potential introduces HIGHER forces than a harmonic
> potential up to 1 Å, but past 1 Å a harmonic potential grows much faster.
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Feb 23 2014 - 12:00:02 PST
