Hi, I am trying to pull/separate a protein dimer by applying constant force in my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set my simulation to run for 5 ns. However, after only 251 ps, I got this fatal error:
Distance of pull group 1 (3.958423 nm) is larger than 0.49 times the box size (16.314939) Can somebody please interpret this error? When I checked the trajectory, the protein seems to be inside the box or at least the COM of the dimer is near the center of the box, so the protein approaching near the boundary can't be the reason for this error. If it can help to clarify, here's my pull code: ; Pull code pull = constant_force pull_geometry = direction ; pull in the direction of pull code pull_dim = Y Y Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = chain_A ; C-terminal of Protein 1 pull_group1 = chain_B ; C-terminal of Protein 2 pull_k1 = -500 ; kJ mol^-1 nm^-1 pull_vec1 = 0 1 0 Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/constant-force-pulling-tp5010180.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
