Hi all I am commencing the initial stages for he calculation of potential of mean force of bringing together two cage molecules. I am following the tutorial in such an exercise at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html In contrast to the tutorial I want to bring the two molecules together along the z axis. I have generated an initial configuration in which the COMs of the two molecules are 5.07 nm apart. In the tutorial to separate a substrate from a protein you use the following parameters in the mdp file.
; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per n pull_k1 = 1000 ; kJ mol^-1 nm^- How should I alter this to pull the molecules together along the z axis? I would've thought the following but I'm not too sure pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_rate1 = -0.01 pull_k1 = 1000 Obviously I have to play with the values, but it is the sign that I'm interested in. Many Thanks Gavin -- gmx-users mailing list gmx-users@gromacs.org http://lists.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
