Carma does what Jason described automatically, namely you can plot the Free
Energy along two or three Principal Components. All you need is to convert
your .prmtop/.nc to .psf/.dcd with cpptraj from AmberTools. Check it out:
http://utopia.duth.gr/~glykos/Carma.html
HTH,
Thomas
On 10 December 2013 22:45, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Dec 10, 2013 at 5:23 AM, anu chandra <anu80125.gmail.com> wrote:
>
> > Dear Amber users,
> >
> >
> > I am working with all-atom MD simulations of protein-ligand system. I
> have
> > carried out PCA analysis after 75ns of simulation. By looking at the
> > collective motions along the first principle component, I could able to
> see
> > that the protein is visiting two different conformations.Now, I am
> looking
> > for a method to capture the free energy landscape of these conformational
> > changes. If I am right, usual methodologies like meta-dynamics. AMD etc.
> > are usually used to overcome the high energy barrier during the
> > conformational changes. Since I could capture the conformational changes
> in
> > my protein during the classical MD itself, it seems like the energy
> barrier
> > is too low between these two different conformations. How can I capture
> > free energy change during these conformational changes? Which method will
> > be helpful for me to do this calculation?
> >
>
> If you have sufficient sampling without using any type of biasing
> potential, you can just calculate free energies directly from the
> simulation.
>
> This is typically done using a histogram along whatever reaction coordinate
> you choose to define and taking the negative log of the histogram
> population (divided by the population of the most populated bin if you want
> to set the minimum energy to 0). Multiplied by -kT, of course...
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 10 2013 - 13:30:02 PST
