<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><br><br></div>