[gmx-users] MD simulation of peptide amphiphile using CG method

[leila karami]

Dear James,

Thanks for your answer.

As I understand, PyCGTOOL generates the coarse-grained molecular dynamics
models from atomistic simulation trajectories. But, I don't want to do
the atomistic simulation.

Also, ATB only generates a complete topology for molecules containing < 40
atoms, while I have 5 PA molecules with > 40 atoms, apiece.

Since my molecules contain amino acids bonded to the hydrocarbon chain
(which are default beads in Martini force field), I think there is
a straightforward way for treatment of that. Unfortunately, I don't have
experience about that. My problem is how to relate amino acids to hydrocarbon
chain?

When I use martinize.py, in structure and topology output files, there are
only amino acids and not hydrocarbon chain.

Should I modify martini_v2.2_aminoacids.itp by adding hydrocarbon tail
parameter to it?

Best,
LK