Aromatic rings don't maintain the planarity during the heating

From: Serena Vittorio (
Date: Fri May 04 2018 - 11:14:30 CDT

Dear NAMD users,
I'm applying MD simulation to a protein-peptide system. During the heating I found that the aromatic rings of the aromatic residues of all the system are distorted, they don't maintain the planarity.
Does anyone know which could be the reason?

Before the heating I ran two steps of minimization, each one for 1000 steps: the first one with the proteins fixed to relax water molecules and the second one with the C alpha fixed. I heated up the system to 300K for 500 ps.
I attached the namd configuration file referred to the heating.


This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:04 CST