[gmx-users] Strange problem.complex out of Box after EM
Dear Gromacs users I am trying to simulate a protein complex. That complex has been obtained after protein-protein docking. I have geneated topology, defined box and solvate, added ions successfully. My complex is centered in box. but when I performed Energy minimization then my protein complex comes out of box from one side. can any body help me in fixing this problem so that i could proceed towards equilibrium steps.. Many thanks with anticipation Regards Saba -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- gmx-users mailing listgmx-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
Re: [gmx-users] Strange problem.complex out of Box after EM
Saba Ferdous wrote: Dear Gromacs users I am trying to simulate a protein complex. That complex has been obtained after protein-protein docking. I have geneated topology, defined box and solvate, added ions successfully. My complex is centered in box. but when I performed Energy minimization then my protein complex comes out of box from one side. can any body help me in fixing this problem so that i could proceed towards equilibrium steps.. There is no problem. It is odd that EM would cause periodicity issues, but suggests that your protein is not centered properly or that your box is not large enough to accommodate it. There may be some inconvenience for visualization (which can be fixed), but there is no such thing as outside in a periodic system. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] Strange problem.complex out of Box after EM
Please change the subject line to the relevant topic and do not paste the entire digest. I guess the archive is already somewhat hopeless, but let's not make it worse :) Saba Ferdous wrote: Dear Justin, I have set 1.5 dodecahedron. i centered the complex in box. complex.gro, complexsol.gro and complex_sol_ions.gro seems inside in box. I m using VMD for visualization. i have rotated it in 3D while when after EM step, i visualize em.gro then half complex seems outside the box. is there any way to center em.gro after energy minimization? Again, this is just a matter of visualization. There is nothing wrong and nothing needed to fix. You can rewrap the periodic cell with trjconv -pbc mol -ur compact if you find you want more convenient visualization. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
