AMBER Archive (2008)

Subject: AMBER: Equilibration protocol for large protein

From: Dmitri Nilov (
Date: Tue Nov 18 2008 - 10:33:26 CST

Hello, my work is focused on MD of rather large protein X-ray
structure (about 800 amino acids),
and I try to use equilibration protocol from tutorial A3: MM-PBSA (I think
it`s actual protocol for explicit water simulations).

Crystallographic water molecules were retained and system was solvated in 12
angstrom TIP3P buffer and neutralized.
After energy minimization of obtained system (at constant volume with 2.0
kcal/mol-A2 restraints on protein) I performed following steps:
1) 50ps of heating from 0 to 300 K (at constant volume with 2.0 kcal/mol-A2
restraints on protein)
2) 50ps of density equilibration (at constant pressure with 2.0 kcal/mol-A2
restraints on protein)

After that the long trajectory of several nanoseconds was computed
successfully (constant pressure, no restrains).
Nevertheless I observe unexpected large interdomain movement of my protein
appeared after 1-2 ns of simulation.
Probably it could be reliable result but it`s raising a doubt.
I`ve checked all output files and energies, temperature, RMSD seem to be OK.
So I`m not shure if presented equilibration protocol quite accurate for my
large system (about 100000 atoms).
Could you help me with any suggestions please?

Dmitri Nilov,
Lomonosov Moscow State University

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