[gmx-users] periodicity and correct output

Shuangxing Dai shuangxingdai at gmail.com
Wed Jul 28 17:35:45 CEST 2010

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?
Shuangxing Dai

On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban <vvchaban at gmail.com> wrote:

> 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 after
> processing negative coordinates are sometimes present as well as those
> bigger than LBOX.
> Vitaly
> Dr. Vitaly Chaban
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