Hi Anna, If there is a representation in which the units are together, then they're together. Trjconv can't put things together which are, in fact, separated.
Cheers, Tsjerk On Tue, Apr 24, 2012 at 12:51 PM, Anna Marabotti <[email protected]> wrote: > 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) > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
