AMBER Archive (2007)

Subject: Re: AMBER: MD_model

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Wed Dec 05 2007 - 17:26:04 CST

Hi Ursula,

normally you would not right away start to simulate your protein at 300K.
First you have to build an input file for amber (you do not specify if you
have an amber prmtop file oder just a pdb file) thinking about things like
solvation model, counterions and ligands. Then most people minimize their
structure for a bit and then slowly (using restraints) heat up and density
equilibrate it. This is most of the time followed by a relaxation phase
until some quantity of interest to you has reached equilibrium and then
your simulation to collect data starts. These equilibration schemes can
be quite complex, depending on the system at hand and the diligence of the
simulator.

So the short answer is: There are many ways to do what you describe,
depending on what the scientific question you are asking is.

The (much) longer answer can be found on the amber tutorial page

http://amber.scripps.edu/tutorials/

which will teach you about preparing a system and running MD simulations
in detail.

Kind Regards,

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Thu, 6 Dec 2007, Urszula Uciechowska wrote:

>
> Dear Amber users,
>
> I have a protein model and I would like to simulate it for about 400 ps at 300K keeping the
> backbone fixed.
> Could someone maybe give me some example o such a input file?
> thank you in advance
>
> Best Regards,
> Urszula Uciechowska
>
> MSc.PhD Student
> Medicinal Chemistry Group
> University of Halle-Wittenberg
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