Ahmet, 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.
deniz. 2010/10/21 ahmet yıldırım <ahmedo...@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 > > -- > Ahmet YILDIRIM > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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