Dear gromacs users, I would like to obtain a potential of mean force (PMF) plot from an AFM Pulling calculation.
I used AFM method in the Pull code to separate two strands of peptides along their center of mass reaction coordinate. here is the parameters I used: runtype = afm ngroups = 1 reference_group = receptor group_1 = ligand reftype = com pulldim = Y Y Y afm_rate1= 0.0004 afm_k1 = 10000 afm_dir1 = 0.2284214 -0.940737 -0.24730 afm_init1 = 0.17445 -0.71846 -0.188685 As you can see, I pulled in all dimensions, and my pdo file contains all three coordinates. I have searched the list but didnt find away to analyze the data to obtain a free energy profile. any help will be appreciated. Belquis _______________________________________________ gmx-users mailing list [email protected] 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
