Questions about equilibration

From: pellegrini (pellegrini_at_ill.fr)
Date: Thu Apr 10 2008 - 10:19:57 CDT

Hello,

I am a beginner with MD simulations and there are some technical points
that I do not
understand when using NAMD.

Basically, I would like to perform several MD simulations at different
temperature.
So, for each MD simulation, I first have to perform an equilibration
step. To do so,

    * I solvated my protein
    * I added the counterions
    * I used the configuration file of example 1-3 of NAMD tutorial
(equilibration of ubiquitin
in a waterbox).

My goal is to perform 100 steps of CG minimization followed by 100 ps
MD. I am currently running
the equilibration and ... it runs !!! but I have two questions:

    -why is it a Langevin MD that is performed ? I thought that this
kind of dynamics aimed to simulate the solvent
effect and in my case (or also ubiquitin example) I do have explicit
solvent.

    -why a Langevin piston is used ? Does it mean that I fixed my
temperature with Langevin dynamics and that I fixed my pressure with
Langevin piston ? Am I doing in such a case a NPT equilibration ? Is it OK ?

thank you very much for your help

Eric Pellegrini
Institut Laue Langevin
Grenoble, France.

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