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 <[EMAIL PROTECTED]>:
> 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 > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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