[gmx-users] periodicity and correct output

Vitaly Chaban vvchaban at gmail.com
Wed Jul 28 17:46:21 CEST 2010

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...


On Wed, Jul 28, 2010 at 6:35 PM, Shuangxing Dai <shuangxingdai at gmail.com> wrote:
> 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,
> 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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