Hi,
> Removing periodicity from the trajectory can be done after simulation
> using g_traj with the "-nojump" option.
Actually,
trjconv -pbc nojump
Cheers,
Tsjerk
>
> Best,
> Lukasz
>
> --
> Lukasz Cwiklik
> http://cwiklik.wordpress.com
> --
> gmx-users mailing list gmx-us...@gromacs.org
>
On Tue, Nov 24, 2009 at 1:09 PM, Omer Markovitch wrote:
> On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin 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"
On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin 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 ha
Chih-Ying Lin 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 th
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. B
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