Hi there, I used the old Gromacs 3.3 for pulling simulations using afm with success. For the new upgrade, I cannot understand the new configuration for the former standard afm constant velocity pulling with one reference group and the pulling group. For example, when the manual says position Pull to the position of the reference group plus pull init + time*pull rate*pull vec.
Where is it pulling? How is that it pulls to the position of the reference group? Wa I have searched the archives for more details of the new convention for pulling simulations but not enough. Here is my pulling code for the .mdp file. ...... pull_geometry = position pull_group0 = a_5 ;the C-alpha pull_group1 = a_757 ;the N-terminal pull_dim = N N Y ;pulling in the Z-direction pull_k1 = 500 ;spring constant? pull_rate1 = 0.05 ;velocity pull_vec1 = 0.0 0.0 1.0 ;direction of the pulling pull_init1 = 1.46 1.19 3.05 ;pulling from the N-terminal, positions respect to the reference group pull_nstxout = 1000 pull_nstfout = 1000 Any comments will be more than welcome Marisa Roman mb...@drexel.edu Physics Dept. Drexel University - Philadelphia - USA _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php