[gmx-users] (no subject)

VENKATESH HARIHARAN vuh105 at psu.edu
Tue Jun 24 14:15:59 CEST 2008


    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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