Dear all, I want to calculate the persistence length of a triple helix. After minimization and equilibration, I did MD simulation without position restraints for atoms. I read the second paragraph of gmx polystat, and understood that for one chain, I can choose its backbone atoms as the index group and got the persistence length. In the description, the persistence length is defined as number of bonds. Can I understand it as the persistence length equals to the number of bonds multiply the bond length? But how can I determine the bond length?
For the triple helix, I think I need to work with the centre of mass of the three backbone atoms in the three chains. The three chains in the triple helix are identical. How can I get the trajectory of the centre of mass of the same backbone atoms(or alpha carbon atoms) in the three different chains? And after getting this trajectory, can I use gmx gangle to calculate the angles and then calculate their cosine values and finally get its persistence length? But how to determine the index file? I want to calculate the angle between every third point of centre of mass. Could anyone help to give me some guidance about how to do this? Thanks in advance. regards -- 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.
