AMBER Archive (2008)

Subject: AMBER: problem with restraints

From: Barbault Florent (
Date: Thu Jul 10 2008 - 13:59:15 CDT


I am facing a problem with AMBER 9.0. I am doing molecular dynamics
with explicit solvent of a ligand/protein structure. I use harmonic
restraints to fix a part of the protein. These restraints are
expressed with this mask: '(:111 >@8.0 & :1-100!@H=)'

The mask contains 718 atoms and should correspond to the heavy atoms
which are far from 8 A of the residue 111.

Generally, I launch 20 runs of 100 ps in order to get 2 ns trajectory.
However, after each restart (irest=1, ntx=7) the restraint energy is
increasing and then the system is instable. This doesn't happen if I
launch 2ns simulation in one time.

Since the reference structure is identical in every running steps, I
don't understand why I get this problem. Any help will be highly

Florent Barbault

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