[gmx-users] gmx trjconv -pbc doesn't work

[Chenlin Lu]

Hello all,


Some of my trajectories has pbc problems. The substrate diffuses out of the pbc box. And I am trying to fix it using gromacs command gmx trjconv -f {}.xtc -s {}.tpr -o {}_nopbc.xtc  -pbc nojump. But the fixed trajectories still have same problems when I check them in VMD. I caculted the gyrations which show there are no significant changes for those fixed trajectoies. Is it because the presentation problem of VMD or gromacs pbc treatments. Any advice? (gromacs pbc treatment and VMD presentaion). Thanks in advance.


Chenlin

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Chenlin Lu

Department of Chemical Engineering, 

Tsinghua University, Beijing, 100084

Tel: 86-13120180517

Email: lucl17 at mails.tsinghua.edu.cn