Hello,
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:
pdb2gmx -f 3B6U.pdb -p protein.top -o protein.gro
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.
______________________________
Venkatesh Hariharan
Schreyer Honors College
Undergraduate - Bioengineering
"You must be the change you wish to see in the world."
--Mohandas Karamchand Gandhi
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