[gmx-users] Fwd: Determine sec structure by MD

[rama david]

Hi Gromacs Friends,

        I have the experimental result of change in Secondary
structure of peptide from random coil to Beta sheet, as  the conc
increases
( but  not know the Parallel or anti-parallel )

                       I run Simulation of ( 30ns ) two peptide in random coil
structure put sufficiently apart  (2.4 nm) so they are not interacting to each
other initially, I found they are coming close to each other in anti-parallel
fashion, But they remain in random coil.To extend these study I run simulation
of four peptide they also come close to each other in anti-parallel way
(Show the change in secondary structure from random coil to
anti-parallel beta sheet)
After these I put the peptide in anti-parallel way  to form the fiber structure,
they show the some parallel and anti-parallel  arrangement in fiber.

Note- If I put the two peptide in random state, close enough in parallel to each
other they also form parallel beta sheet structure ..
As the MD study is affected by initial arrangement.

I am interested How to Determine by Molecular Dynamics, Is  structure
favor Parallel
or Anti-parallel state ?????  also the energy difference in two,
parallel  and anti-parallel ????

Please give me some some valuable suggestion and method to solve my query.

Thank you in advance


Have a nice day
With Best Wishes and Regards
Ramadavid