Question about trajectory file visualization.

Dear lammps user,
I have a question about trajectory file visualization. I’m doing diffusion coefficient calculation. The question is that when I was load the trajectory file by vmd, the atoms in the box are moving along a direction. I checked the coordinations of the atoms in my system, and on coordinations out of the box. Can any one tell me what happen to my system? Thanks!

(The picture scene and scene1 show the movement of the box, I’m sorry I can’t upload the movie because of the size imitation.)

Kerwin

vmdscene.jpg

vmdscene1.jpg

Dear lammps user,
I have a question about trajectory file visualization. I’m doing diffusion coefficient calculation. The question is that when I was load the trajectory file by vmd, the atoms in the box are moving along a direction. I checked the coordinations of the atoms in my system, and on coordinations out of the box. Can any one tell me what happen to my system? Thanks!

you probably have a center-of-mass drift in your system. this can be due to your initialization. the velocity command has an option to remove such momentum. you may have to investigate your simulation settings, if this re-appears, as it may be an indication of systematically unbalanced errors. and if this is all not helping, you may want to look into fix momentum, which can suppress this symptom.

axel.

Thanks, Axel! I’m going to try what you said.

Dear lammps user,
I have a question about trajectory file visualization. I’m doing diffusion coefficient calculation. The question is that when I was load the trajectory file by vmd, the atoms in the box are moving along a direction. I checked the coordinations of the atoms in my system, and on coordinations out of the box. Can any one tell me what happen to my system? Thanks!

you probably have a center-of-mass drift in your system. this can be due to your initialization. the velocity command has an option to remove such momentum. you may have to investigate your simulation settings, if this re-appears, as it may be an indication of systematically unbalanced errors. and if this is all not helping, you may want to look into fix momentum, which can suppress this symptom.

axel.