Hi Melchor, So what did you expect, what did you do, and what did you get?
Cheers, Tsjerk On Tue, Jul 2, 2013 at 2:45 PM, Melchor S. <msm...@cid.csic.es> wrote: > 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 > -- Tsjerk A. Wassenaar, Ph.D. -- 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
