Boundaries of the box used for visualisation are totally arbitrary, it makes not difference when the various simulations are being performed. Most efficient to simply process it at the end to get the visual representation you want
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 24 Apr 2020 at 12:29, Mohamed Abdelaal <m.b.abdel...@gmail.com> wrote: > Hello everybody, > > I know that due to periodic boundary conditions the molecules move from one > side of the box to the other side and moves outside the box. I also know > how to use trjconv to solve this problem and I usually do this step at the > end of the simulation. However I have noticed that after the energy > minimization, some molecules which were position restrained at the bottom > of the box have been moved to the top of the box. I knew that I have this > periodic boundary condition problem not just from visualization of the > structure after the energy minimization, but also from the atoms > coordinates in the .gro file after the energy minimization, the z > coordinate of some atoms have been changed from bottom to top as below: > > before energy minimization: (the z coordinate was always zero) > > 1GRM C1 1 0.061 0.071 0.000 > 1GRM C2 2 0.184 0.142 0.000 > 1GRM C3 3 0.184 0.284 0.000 > 1GRM C4 4 0.061 0.355 0.000 > 2GRM C1 5 0.061 0.497 0.000 > > > after energy minimization: (z coordinate of some atoms have been changed > into 14 which is at the top of the box) > > 1GRM C1 1 0.061 0.071 14.000 > 1GRM C2 2 0.184 0.142 14.000 > 1GRM C3 3 0.184 0.284 0.000 > 1GRM C4 4 0.061 0.355 0.000 > 2GRM C1 5 0.061 0.497 14.000 > > > > Do I need to solve this PBC problem between the different steps (energy > min, NVT, NPT, production run) or it is okay to continue my simulation > (even if the molecules have moved) and solve this problem at the end ? > > Many thanks, > Mohamed > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
