AMBER Archive (2008)

Subject: AMBER: periodic boundary

From: Sally Pias (
Date: Wed Dec 31 2008 - 02:37:25 CST

I am using a truncated octahedral TIP3P water box to solvate a protein
and am running constant volume molecular dynamics simulations with
periodic boundary. I have added solvent in a 10 Angstrom radius
around the protein and have carefully equilibrated the system. One
part of the protein is fairly mobile and, at certain time points,
appears to protrude out of the solvent box upon reimaging with the
ptraj command 'image center familiar.' I do not see any remarkable
changes in the energy of the system at these time points, and I
suspect that this is an imaging problem, rather than a solvation
problem. However, the radius of the solute changes substantially over
the course of the simulations, so I want to be sure I have added
enough solvent.

What is a good way to check whether my system has remained properly
solvated? Is the radius of the solvent box versus the radius of the
solute a good measure? My periodic box is around 70 Angstroms in
diameter, and I am using a nonbonded cutoff of 10 Angstroms. How far
can my protein elongate and still remain properly solvated in this
box? It is probable that the protein could extend to double its
original diameter during longer simulations. Would I be better off
using implicit solvation for a system that is changing conformation so

Thank you in advance for any help.

Sally Pias
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