[gmx-users] (no subject)

Lee Soin nomadoro at gmail.com
Wed Jun 25 09:22:39 CEST 2008

Hello, Venkatesh Hariharan!
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.
2008/6/24 VENKATESH HARIHARAN <vuh105 at psu.edu>:

> 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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