Hi Shuangxing,
For my case, I wrote a script just to do +/- LBOX when xLBOX || 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 PM, Shuangxing Dai shuangxing...@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 vvcha...@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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