set iwrap=0 in your mdin file. iwrap "wraps" molecules that leave the box
into the other side.
On Thu, Nov 19, 2009 at 6:30 PM, Chih-Ying Lin <chihying.usc.edu> wrote:
>
>
> Hi
> With the periodic boundary condition, all the recorded coordinates of the
> atom are within the simulation box.
> To calculate the MSD, the movement of the center mass of the molecules
> between this time step with the next time step is calculated without
> considering the periodic boundary condition.
>
>
> But all the recorded coordinates of the atom are within the simulation box
> after considering the periodic boundary condition.
> So, how can I remove the periodic boundary condition to get the truly
> movement of the atoms between the two time steps ?
>
>
> Thank you
> Lin
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 19 2009 - 16:30:02 PST
