<div>Hello, Venkatesh Hariharan!</div>
<div>To perform AFM pull you should provide an additional input file named xxx.ppa and append "-pi xxx.ppa" to mdrun arguments. You can read GROMACS online or paper manual for detail.<br></div>
<div class="gmail_quote">2008/6/24 VENKATESH HARIHARAN <<a href="mailto:vuh105@psu.edu">vuh105@psu.edu</a>>:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>Hello,<br><br> I am new to GROMACS, and so my questions my seem relatively simple. I'm attempting to use the AFM Pulling facet of the program to generate force extension curves of ~20 amino acid polypeptide chains. After cutting down my .pdb file to the desired amino acids, i used the command:<br>
<br>pdb2gmx -f 3B6U.pdb -p protein.top -o protein.gro<br><br>The command generated the required gromacs files. Now, I am unsure of the next step. Would it be to create a .mdp file with my specified parameters? If so, what command should I use after creating the .mdp to start the simulation? Is there an AFM Pulling / Force Extension Curve tutorial available? Thanks.<br>
<br>______________________________<br><br>Venkatesh Hariharan<br>Schreyer Honors College<br>Undergraduate - Bioengineering<br><br>"You must be the change you wish to see in the world."<br>--Mohandas Karamchand Gandhi<br>
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