Hi,
Thanks to all for the valuable suggestions. I will carefully look in to
your replies.
Thanks once again.
Regards
Anu
On Wed, Dec 11, 2013 at 2:56 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> BTW: careful with PCAs...
>
> First, make sure that the PCAs you choose represent a substantial amount
> of the variance. Too many papers show 1 or 2 PCAS and the sum of them is
> only 20% of the variance. Granted, it is the top 20%, but even then, it
> is a small part of the story.
>
> Second, PCAS are notoriously hard to converge. Do this: take your 75 ns
> MD, split in into 2 halves. Redo PCA for each half separately and see if
> the first PCA vector for one half is similar to the first PCA vector for
> the second one. If not, then your PCA vecotr for the free energy is very
> arbitrary and does not tell you too much about your system.
>
> Adrian
>
> On 12/10/13 3:59 PM, Thomas Evangelidis wrote:
> > 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
> >>
> >
> >
>
> --
> Dr. Adrian E. Roitberg
>
> Colonel Allan R. and Margaret G. Crow Term Professor.
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Wed Dec 11 2013 - 06:00:08 PST
