Hi all, I am trying to calculate an RMSD of two simulations. All the setting are equal for both, but i use OPLS in one and for the other gromos53a6.
I wanted to calculate the RMSD between the trajectory and the crystallographic structures(Open and closed forms). The simulation involves a protein that starting from a closed conformation, opens the active center after some ns. So I expect a very small RMSD at the beginning , that then will increase, compared to the closed form, and when I calculate the RMSD, respect to the open form, the opposite. With OPLS both using VMD and g_rms, I obtain the expected RMSD ( I run two simulations with succes), but with Gromos96 53a6 no. I have made three different simulations with gromos53a6, changing the initial velocities, but I don't have any succes. I don't know what could be the reason, some of you have had this problem previously? Any solution a part of try with another ff? Thanks in advance, PD: For if can help to find a solution: Settings of the simulation Rhombic dodecahedral box with SPC water model was used. T= 300K, P=1bar using a Berendsen thermostat (with time constant τt = 0.1ps)-barostat with an isotropic compressibility of 4.5·10-5 bar-1 and time constant of 0.5 ps. Time step of 2 fs, constraining bond lengths with LINCS. For compute the long range coulomb electrostatic, I use PME with a grid of 1Å. For the Van der Waals interactions I use switch function between 0.8 and 0.9 nm. How I do it I minimize the energy of the solvated protein with the steepest descent algorithm. Then I run a MD simulation at 300K using harmonic position restraints on the heavy atoms of the protein with a force constant of 1000 KJ mol-1 nm-2. Then, I performe a simulating annealing from 0 to 300K and fiinally, I run the "production" molecular dynamics starting from the SA trajectory. For analize the trajectory succesfully, I use the pbc nojump and fit rot+trans options. Melchor S. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-calculating-RMSD-with-gromos-tp5009494.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
