On Sun, Feb 23, 2014 at 12:48 PM, Ali M. Naserian-Nik <naseriannik.gmail.com
> 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 - 10:30:02 PST
