> 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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Received on Thu Dec 04 2014 - 14:00:02 PST
