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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
