Re: Basic question.

From: Peter Freddolino (
Date: Fri May 26 2006 - 21:41:43 CDT

Hi Taeho,
to answer (2) first, equilibration is a short molecular dynamics
simulation designed to relax the initial configuration; for example, it
lets dipoles orient properly and water find more appropriate positions.
The only technical difference is that it is sometimes carried out with
restraints on part of the system (often the protein, for example). This
step is necessary to avoid any artifacts that might show up from
starting to take data from a system that is going to undergo quick
relaxations such as this. I would highly recommend to you a textbook on
molecular modelling techniques (such as Leach's /Molecular Modelling:
Principles and Applications/) to have a look at the need for this step
in more detail.

Taeho Kim wrote:

>Dear all.
>I have some basic question.
>1. Why do we have to do equilibration step?
>2. What is different between equilibration and molecular dynamics?
>I have stuied about that by using Namd tutorial. I couldn't understand
>Thank you.
>Best regards...

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