Dear gromacs users, I have done simulations for 100ns. My peptide length is 25 residue length. While calculating the RMSD by executing the gmx rms I have used 2 C-alpha atoms at N-terminal and one C-alpha atom at C-terminal for least square fitting and then calculated the RMSD for the rest of the C-alpha atoms. Among the frames some frames got more than 2nm RMSD with respect to starting structure. I have doubt here. 2nm means (20 Angstrom) is very high, is it possible to get this mush deviation with respect to starting structure? If it is yes, what is the reason for deviation?
Thanks in advance Surya Graduate student India. -- 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.
