Re: [gmx-users] periodicity and correct output

Yes, mdrun applies PBC at every step and some atoms at top/bottom will translate to the bottom/top at some steps. So in dynamics simulation, the polarization given by gromacs is meaningless. Is there anyway I can apply PBC without translation ( e.g. change the box center automatically to avoid tran

Re: [gmx-users] periodicity and correct output

Hi Shuangxing, For my case, I wrote a script just to do +/- LBOX when x>LBOX || x < 0. I am not well familiar with polarization algorithm in gromacs but it seems not to be a problem during a run since mdrun applies PBC at every step. Maybe I am false here... Vitaly On Wed, Jul 28, 2010 at 6:35

Re: [gmx-users] periodicity and correct output

I think I met the same problem. When apply periodicity to the system, some atoms will translate to the other side of the box, and this gives wrong polarization values (especially in dynamic simulations). Anyone has idea how to prevent this and get correct polarization in dynamics? Thanks, Shuangxin

[gmx-users] periodicity and correct output

Hi, Is there an option in any gromacs utility to apply periodicity to the output configuration or trajectory? I want to get all the coordinates just within an elementary box, between 0 and LBOX in spite of any details of the system. For example, "editconf -no(pbc)" does not do its work since afte