Re: [gmx-users] Diffusion beyond periodic boundary

2013-02-09 Thread Kenji Mochizuki
cific molecule for "-pbc nojump" ? >> > For example, >> > the coordinates of water molecules are rewind and the LJ particles are NOT >> > rewind ? >> > >> > Regards >> > >> > Kenji >> > >> > - Original Message - >> &g

Re: [gmx-users] Diffusion beyond periodic boundary

2013-02-09 Thread Tsjerk Wassenaar
k Wassenaar > >> To: Discussion list for GROMACS users > >> Date: 2013-02-09 17:24:23 > >> Subject: Re: [gmx-users] Diffusion beyond periodic boundary > >> > >> Hi Kenji, > >> > >> You can remove the jumps/rewinds using 'trjconv -

Re: [gmx-users] Diffusion beyond periodic boundary

2013-02-09 Thread Kenji Mochizuki
>> From: Tsjerk Wassenaar >> To: Discussion list for GROMACS users >> Date: 2013-02-09 17:24:23 >> Subject: Re: [gmx-users] Diffusion beyond periodic boundary >> >> Hi Kenji, >> >> You can remove the jumps/rewinds using 'trjconv -pbc nojump&#x

Re: [gmx-users] Diffusion beyond periodic boundary

2013-02-09 Thread Tsjerk Wassenaar
Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki wrote: > Dear All > > I have performed MD run with periodic boundary condition, > which system is consist of water and LJ particles. > > I would like to know

[gmx-users] Diffusion beyond periodic boundary

2013-02-08 Thread Kenji Mochizuki
Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the dis