Hi Sogol, You remove jumps over periodic boundary conditions, giving a continuous trajectory. That gives you a very nice view on diffusion in your system, which happens to be equal in all directions. Hence, the end result looks spherical. But that's not the same as having a spherical box. If you draw the box in VMD or Pymol, you'll see it's still close to the original (triclinic) shape, but has become a bit small in relation to your molecules.
Cheers, Tsjerk On Wed, May 16, 2012 at 11:49 AM, Kowsar Bagherzadeh <[email protected]> wrote: > Dear users, > > I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 > K. after 1ns of simulation in 300 K, the protein jumps out of the box and > when I use the command > > trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump > > followed by > > trjconv_mpi -f new*.trr -s *.tpr -o new*.pdb -dump 1000 > > the box shape changes from dodecahedron to spherical. In Gromacs manual I > read ; > > " There are several possible shapes for space-filling unit cells. Some, as > the rhombic dodecahedron and the truncated octahedron approach a spherical > shape better than a cubic box and are therefore more economical for studying > an (approximately spherical) macromolecule in solution, since less solvent > molecules are required to fill the box given a minimum distance between > macromolecular images....... ". > > Does it mean that it is ok and I can continue the simulation or I have to > increase the box size? After simulation in 200 K the protein juped out of > the box but using the same command the problem was fixed, without changing > the box shape. > Thank you in advance for the help > > Sogol > > > -- > 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
