[gmx-users] persistence length of triple helix

[Ming Tang]

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