Re: lengthening time-step with constraints causes RMSD "jump"

From: Jim Phillips (
Date: Thu Jun 02 2011 - 15:36:33 CDT

On Thu, 2 Jun 2011, P.-L. Chau wrote:

> I froze the atoms in the initial stages of the simulation, but as the
> initialisation of the protein simulation progresses, I gradually relax the
> constraints on the protein atoms. Initially I use strong constraints, and
> I plan to relax the constraints as I go along. So I am afraid I cannot get
> away from "strong" constraints using this initialisation scheme. Could I
> ask you what you might suggest as an alternative initialisation scheme,
> please?

If your restraints are so strong that you require a .2 fs timestep then
they are more rigid than a covalent bond. Why would you care that the
protein is not fixed if it can only move .1 A?

Is your BOUNDARY energy the same before and after restart?

The other possibility I can think of is that there is something wrong with
your structure that requires these small timesteps, not the restraints.

Are you using constant pressure at this point? That could also cause
problems as the cell size fluctuates and rescaling the atom coordinates
jerks them around their restraint points.


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