Thanks Jason for your valuable suggestion.
On Thu, Dec 4, 2014 at 11:33 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> > On Dec 4, 2014, at 4:18 PM, Kshatresh Dutta Dubey <kshatresh.gmail.com>
> wrote:
> >
> > Hi Jason,
> >
> > Thanks for your reply. The single point energy of two states and then
> their
> > difference as free energy, I think, doesn't seem very interesting without
> > proper sampling. I am looking something like umbrella sampling or Steered
> > MD. But in amber advanced tutorial/manual, I didn't get information to
> put
> > one state/coordinate as a reference and to drive initial structure
> towards
> > reference so that we can get the potential of mean force for this
> > conformational transition as we can get in umbrella sampling. So, is
> there
> > any way in this direction? I found in NAMD, one can define collective
> > variables but I am easy with amber and wiling to do similar calculation
> > using Amber.
>
> The NMR restraints commonly used in Amber (distance, angle, dihedral,
> etc.) *are* collective variables -- they’re just very simple ones. They
> are analytical, differentiable functions of atomic coordinates, and so can
> be used to form a restraint with the force determined analytically through
> the chain rule. NAMD and other packages (e.g., those that link to plumed)
> support more exotic colvars, like radius of gyration and RMSD, perhaps, but
> the basic idea is the same. (In fact, Amber supports somewhat more complex
> colvars through its NMR restraint functionality, like linear combinations
> of distances, plane-point restraints, and plane-plane restraints... in
> sander at least).
>
> There is also the ABMD functionality which defines a set of collective
> variables you can use as restraints (radius of gyration, multiple RMSDs,
> number of bonds, etc.), also only in sander -- see section 21.6.2 in the
> Amber 14 user’s manual (page 384).
>
> You may also want to consider targeted MD, which I believe uses an
> RMSD-based restraint to drive one structure toward another. More details
> are given in the manual.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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>
--
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel
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Received on Thu Dec 04 2014 - 14:00:02 PST
