[gmx-users] published paper related to protein simulation using gromacs

Deniz KARASU karasudeniz at gmail.com
Thu Oct 21 13:27:27 CEST 2010


For starting you can read Leach's  book (Molecular modeling: principles and
applications). This book gives you theoretical background and opinion about
application areas of molecular dynamics (MD) simulation. Gromacs is only a
simulation tool to do MD simulation, after understanding MD you can use any
simulation tool (gromacs, namd, amber ..)  to do MD.     Also you can look
some review papers on molecular dynamic simulation  like Lindahl's paper
(do:10.1007/978-1-59745-177-2_1),  Karplus's paper (doi:10.1038/nsb0902-646.) .
Lindahl's paper has a introduction format and prepared like tutorial for
gromacs. For more paper using gromacs you can search google scholor with
"gromacs" keyword.


2010/10/21 ahmet yıldırım <ahmedo047 at gmail.com>

> Dear Gromacs users,
> I am new user Gromacs. I want to study on protein simulation using gromacs.
> If possible, Can you send a few articles on the protein simulation using
> Gromacs?For example, I downloaded from Protein Data Base the PDB extension
> file of any protein. What is the purpose of protein simulation?What is
> commonly the forcefied used for protein simulation? Which parameters are
> calculated?... To answer these questions, I need the articles/papers
> written in this area.
> I will be happy if you help
> Thanks in advance
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