[gmx-users] Studying protein folding: An approach

Rodrigo Faccioli rodrigo_faccioli at uol.com.br
Tue Apr 19 18:55:56 CEST 2011

Hello Miguel Quiliano,

I have been working with Protein Structure Prediction. But, my research is
computation area which means to develop an algorithm to try study it.

Maybe the paper below helps you.

Reproducible Polypeptide Folding and Structure Prediction using Molecular
Dynamics Simulations
M. Marvin Seibert, Alexandra Patriksson, Berk Hess and David van der Spoel

You can find more details about mdp file in

I hope these information help you.

Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5

On Tue, Apr 19, 2011 at 12:53 PM, Miguel Quiliano Meza <rifaximina at gmail.com
> wrote:

> Dear Community.
> I am a beginner user of Gromacs for this reason I would like to consult my
> case.
> Nowadays, I am studying a protein which folding process has experimental
> data (especially for a mutant). Structural information about how a mutant
> destabilizes secondary structure was recently published. The work shown
> how gradually increasing 1  C degree the structure is affected (from 18 to
> 20 C).
> I would like to study the process in silico, but I don´t know what
> parameters put in the ".mdp" file.
> Please their advices or help would be appreciated.
> Best Regards.
> Miguel Quiliano
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