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
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
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
3 matches
Mail list logo