[gmx-users] maintaining the overall conformation of a protein during simulation

[Mark Abraham]

----- Original Message -----
From: Lee Soin <nomadoro at gmail.com>
Date: Saturday, March 7, 2009 19:05
Subject: [gmx-users] maintaining the overall conformation of a protein	during simulation
To: gmx-users at gromacs.org

> Hello!
> I want to maintain the overall conformation of a protein during simulation. Is it recommended that I 
> (1) use distance restraint generated by genrestr -disre
> (2) use distance constraint generated by genrestr -constr
> or
> (3) specify in [ bonds ] type 6 for each pair of C-alpha atoms

"Restraints" and "constraints" are distinct phenomena in GROMACS. Check out the manual here.

A minimalist approach is often a good idea - you don't want to perturb your physical model further from realistic than it already is. Consider (or experiment) on how it might unravel, and consider some distance restraints that would counter those. Frankly, if it does unfold under the lifetime of your simulation, and it should be stable, then your forcefield has failed and that might be an interesting result in its own right.

Mark