Hello, I was running different simulations with the following pull code
1/ ;-----------PULL CODE --------------------- pull = umbrella pull_geometry = direction pull_group1 = r_535 pull_vec1 = 0.51 0.026 0.273 pull_k1 = 110 pull_rate1 = 0.002 ; nm/ps = 20 A/ns pull_start = yes pull_init1 = 0 2/ Different pull group ;-----------PULL CODE --------------------- pull = umbrella pull_geometry = direction pull_group1 = r_538 pull_vec1 = 0.51 0.026 0.273 pull_k1 = 110 pull_rate1 = 0.002 ; nm/ps = 20 A/ns pull_start = yes pull_init1 = 0 3/ Two pull groups ;-----------PULL CODE --------------------- pull = umbrella pull_geometry = direction pull_ngroups = 2 pull_group1 = r_533 pull_vec1 = 0.51 0.026 0.273 pull_k1 = 110 pull_rate1 = 0.002 ; nm/ps = 10 A/ns pull_init1 = 0 pull_group2 = r_538 pull_vec2 = 0.51 0.026 0.273 pull_k2 = 110 pull_rate2 = 0.002 ; nm/ps = 20 A/ns pull_init2 = 0 pull_start = yes Additionaly I`ve added the following lines to each file comm-mode = angular nstcomm = 10 I have constructed the pull vector by taking the coordinates of CA of pull_group and coordinates of OW in a water molecule that was positioned in the direction I wanted to pull. Finally, I have calculated the vector by substraction (x2(water) - x1(CA_aminoacid); y2-y1; z2-z1). Observing the results of my simulation I have observed two problems: 1/ Groups are pulled not exactly in the same direction differing by about 45 degrees. I guess that means that system is rotating even though I set comm-mode to angular!!! 2/ The first 5 ns I see no indication of pulling and the force is climbing evenly. Then I see a huge force leap up followed by a leap down (in some picoseconds) corresponding to displacement of pull group. I just don`t understand why force is growing so fast. What am I doing wrong? Any suggestions? Thank you. I appreciate your time. SDA _______________________________________________ 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