Hi all, I¹m looking to run MD simulations of regions of a collagen molecule. A whole collegen molecule is made up of three polypeptide chains, each around 1000 residues long (gross generalisation as there are around 24 different collagen protein families). I am only interested in modelling a section of 30 residues in length, and then as a dimer (30 per chain, three chains per molecule, 2 molecules to make the dimer, 180 residues in the whole system)
I tried looking at the structure as a free-floating dimer in solvent. Two things occurred, 1) they became monomeric, 2) the system box had to be over twice the size in all three dimensions to consider all of the possible conformations without seeing its period image. This went from being a very small system to a very large system due to the solvent. After some careful consideration I think my best approach would be to turn each 30 long residue into a polypeptide chain which covalently binds back onto itself, giving the illusion of a very long polypeptide chain. Are there any tutorials of best practice on this techniques, and in particular how to manage the pressure on the adjusting volume? Many thanks Anthony Dr Anthony Nash Department of Chemistry University College London -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
