AMBER Archive (2009)
Subject: [AMBER] equilibration stops for dimer simulation with REMD
From: Sunita Patel (sunita_iitb_at_yahoo.com)
I am trying to simulate a dimer using implicit solvent model (generalized-Born solvation model) with replica exchange molecular dynamics at 16 different replicas. I am using AMBER10. The total number of atoms of the system are 4135. I set up the system for 200 ps equilibration at different replica temperatures after the minimization. The equilibration stops after completing 40ps. However, for the monomer of the same protein, it works fine without any problem.
Could anyboby suggest what would be the problem ? When I saw the 40ps equilibration trajectory in VMD I didn't see anything wrong in the structure. The dimer structure is intact.
Your suggestion will be highly appreciated.