Ahmet,<div><br></div><div>For starting you can read Leach's book (<font face="verdana, arial, helvetica, sans-serif">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:</font><span style="font-family: Myriad, 'Trebuchet MS', sans-serif; line-height: 17px; ">10.1007/978-1-59745-177-2_1),</span><span style="font-family: Myriad, 'Trebuchet MS', sans-serif; color: rgb(153, 153, 153); line-height: 17px; "> </span><span style="font-family: verdana, arial, helvetica, sans-serif; "> Karplus's paper (</span><span style="font-family: Verdana, Arial, Helvetica, sans-serif; ">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. </span></div>
<div><font face="Verdana, Arial, Helvetica, sans-serif"><br></font></div><div><span class="Apple-style-span" style="font-family: verdana, arial, helvetica, sans-serif; ">deniz. </span></div>
<div><span style="color:rgb(153, 153, 153);line-height:17px"></span><br><div class="gmail_quote">2010/10/21 ahmet yıldırım <span dir="ltr"><<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Gromacs users,<br><br>I am new user Gromacs. I want to study on protein simulation using gromacs. If possible, <span lang="en"><span title="">Can you send a few articles on the protein simulation using Gromacs?</span></span>For example, I downloaded from Protein Data Base the PDB extension file of any protein. <span lang="en"><span title=""></span></span>What is the purpose of protein simulation?What is commonly the forcefied used for <span lang="en"><span title="">protein simulation?</span></span> <span lang="en"><span title=""></span><span title="">Which parameters are calculated?...</span></span> <span lang="en"><span title="">To answer these questions, I need the articles/papers written in this area</span></span>.<br>
I will be happy if you help<br>
<br>Thanks in advance<br clear="all"><font color="#888888"><br>-- <br>Ahmet YILDIRIM<br>
</font><br>--<br>
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