Hi Anna, Jumps like that are a consequence of PBC. Nothing wrong. Removing jumps like you did is the proper treatment.
Cheers, Tsjerk On Dec 20, 2011 9:27 PM, "Anna Marabotti" <anna.marabo...@isa.cnr.it> wrote: ** Dear gmx-users, I've just finished several simulations of 4 single point mutants of my dimeric protein in rhombic dodecahedron box (-d 1.5 nm) centered on the protein, filled with water, neutralized with sodium, simulated with Gromacs 4.5.3 for 30 ns after NVT and NPT dynamics. I made simulations in the same way and with the same settings, obtaining 4 trajectories. When I obtained trajectories, I used trjconv to reset the visualization of my systems: trjconv -f traj.xtc -s traj.tpr -pbc mol -ur compact -o traj_mol.xtc (selecting 0=System when prompted) then I used g_mindist to calculate minimum distance between periodic images. The resulting graphs showed me that for all simulations the distance is never lower than 2.0 nm, but for only one system there are some spikes in the final part of the simulation (between 25 and 30 ns) lowering the min distance below 1 nm (only in correspondence of these spikes). I also calculated the rmsd using as reference the .gro file obtained in this way (as suggested sometimes ago by somebody of you, perhaps Justin or Tsjerk): editconf -f traj.tpr -o traj_0ns.gro trjconv -f traj_0ns.gro -s traj.tpr -pbc mol -ur compact -o traj_mol.gro (selecting 0=System when prompted) then: g_rms -f traj_mol.xtc -s traj_mol.gro -o traj_mol_rms.xvg (selecting 4=Backbone when prompted) I see a quite stable rmsd around 0.2 nm for all systems, with spikes up to 4 nm in the same system that showed problems with g_mindist, in positions corresponding to the spikes in the g_mindist.xvg graph. Looking at this trajectory with VMD, I saw that in correspondence with the spikes, the two monomers of the protein "dissociate" and appear in different parts of the simulation box (i.e. my periodic image is formed by one monomer, and another monomer is seen in correspondence with another periodic image). All the other systems move into the periodic box, without "dissociating" into monomers. In order to manage this issue, I applied nojump to the trajectory of this "anomalous" system: trjconv -f traj_mol.xtc -s traj.tpr -pbc nojump -o traj_molnoj.xtc When I repeated the analyses with g_mindist and g_rms, I see graphs perfectly superimposed to the former graphs, except for spikes that have been disappeared. What I would like to know is: - Did I make the correct procedure to treat these systems? - Can I compare the results obtained on this -mol + -noj trajectory with the other trajectories -mol only? - In your opinion, is the "dissociation" of the two monomers only a problem of visualization (given that this protein "behaves" apparently normally after applying pbc nojump), or I have to suppose that this system is anomalous only for this fact? Any help would be very appreciated. Many thanks in advance and best regards Anna __________________________________________________________________ Anna Marabotti, Ph.D. Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with the gun is a dead man" (Roberto Benigni, about Roberto Saviano) -- 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
-- 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