[gmx-users] g_msd => The MSD and periodic boundary condition

[Lukasz Cwiklik]

On Tue, Nov 24, 2009 at 1:09 PM, Omer Markovitch <omermar at gmail.com> wrote:
> On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
>>
>> So, how can I remove the periodic boundary condition to get the truly
>> movement of the atoms between the two time steps ?
>
> Removing PBC and placing atoms back into their "true" location is easy. In
> general, if an atom has moved more than half of the box between two
> consecutive timesteps then it has "jumped" over the box.
> You can see for example eq. 19 & 20 in doi:10.1063/1.2968608 .
> --Omer.

Hi,
Removing periodicity from the trajectory can be done after simulation
using g_traj with the "-nojump" option.

Best,
Lukasz

-- 
Lukasz Cwiklik
http://cwiklik.wordpress.com