Dear gmx-users, I know that this is one of the most frequent subjects in the gmx-users list, however please let me ask you for a direct answer, since it seems to me that this particular question was not treated before. I'm performing MD simulations on a dimeric protein, using a rhombic dodecahedric box. I made 3 simulations in which my system was subjected to different isotropic pressures (first simulation: room pressure; second simulation: small increase of pressure; third simulation: big increase of pressure). I run 50 ns simulation for each system, and at the end of simulations I checked for the visualization of the system with VMD and for the RMSD against the starting configuration. Using g_rms command, I checked for the backbone RMSD against starting structure (fullMD.tpr file). The first system stabilized after a few ns of simulation, and then the RMSD remained constant. The second system stabilized after a few ns of simulation, but with a quantity of "spikes". The third system stabilized after a few ns of simulation and then, at about 30 ns of simulation, the RMSD value jumped on from approx. 0.4 nm to > 4 nm and stayed stable on that new value until the end of simulation. I had a look at this trajectory with VMD, and saw that the dimeric protein separates into two monomers. This phenomenon is consistent with some experimental data about the protein, and it seems to me consistent also with the RMSD trend found on the trajectory. However, due to visualization problems with my rhombic system, I decided to apply trjconv -pbc nojump: trjconv -s fullMD.tpr -f fullMD.xtc -o fullMD_noj.xtc -pbc nojump (choosing System=0 as option) After this action, I re-calculated the RMSD of the simulations using the same options as before...and found that in the third simultion the RMSD is no longer jumping on to > 4 nm. The visualization of the trajectory shows the protein in form of a dimer that fluctuates into the zone of "spreaded" solvent (no longer a box). My question is: was the separation into two monomers a simple artifact of the simulation, corrected by trjconv, or is trjconv able to affect the results of the system in such a way that when monomers truly separate, trjconv is able to "force" them together again? How can I check for these two possibilities? Finally: in this last case, can you suggest me other ways to manage the trajectories in order to remove the spikes related to jump across the periodic boundaries? Thank you very much for help, and best regards Anna ____________________________________________________ Anna Marabotti, Ph.D. Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with a gun is a dead man" (Roberto Benigni, about Roberto Saviano)
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