Dihedral interactions in polymers

Dear LAMMPS developers/users.

I am interested in assessing helicity of a polymer without using dihedrals – only bonds and angle potentials. Now of course to further analyse the data (say in VMD) I would need to have the dihedrals if I wanted to say build a Ramachandran plot or assess the helicity of the structure. So my question is rather simple conceptually: can I somehow output dihedral data without having to actually put in any constraints on dihedral interactions?

Thank you for any help in advance!

Anna

dear anna,

Dear LAMMPS developers/users.

I am interested in assessing helicity of a polymer without using dihedrals
-- only bonds and angle potentials. Now of course to further analyse the
data (say in VMD) I would need to have the dihedrals if I wanted to say
build a Ramachandran plot or assess the helicity of the structure. So my
question is rather simple conceptually: can I somehow output dihedral data
without having to actually put in any constraints on dihedral interactions?

if your bond topology doesn't change, there is no need to have any
dihedral information present during simulation.
in the case of VMD, you can simply reconstruct the topological
dihedrals after the fact from the bond topology (e.g. via the
topotools plugin) and then do your analysis.

axel.

Dear Axel,

Firstly, thank you for your support for the past 6 years, through my degree, my PhD and even a post doc!

Thanks for your help with this particular question; It helped to see that topotools is such a versatile and a nice tool to use. I will need to learn more about how to solve the exact issue (due to formatting in the output dump files), but I found the information on your topotools website.

With best wishes
Anna