Hello everyone, I'm trying to compute the PMF for pulling two proteins apart. I'm planning on setting up several runs where the COM separation of the proteins is constrained and the constraint force is measured over the course of a long simulation. However, I'm having trouble doing this because I'm unsure of the inputs in the .ppa file. I'm trying to do this with Gromacs 3.3.3. Here is the .ppa file I'm using:
runtype = umbrella ngroups = 1 reference_group = knob reftype = com pulldim = Y Y Y group_1 = car k1 = 1000 pos1 = 0.0 0.0 28.8989219666 Here, there are two proteins: car and knob. The COM of car is located at (0.0 0.0 28.8989219666) relative to knob. The problem I'm experiencing is that the simulation results in the two proteins being pulled apart instead of constrained at distance pos1. I believe that I'm misinterpreting the inputs. Does anyone know the solution? Thanks, Bob _______________________________________________ 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