How to Avoid FENE Bond Cross Talk

LAMMPS LAMMPS Mailing List Mirror
1

Dear All,

I use moltemplate to create 10 beads, eight backbones and two end beads:

then use this small system to build a larger system. After using soft
potential to relax
the system, I use VMD to see the process and find that the bonds are cross
talk:

How to avoid this?

there is nothing to avoid. instead, you have to learn to understand
how VMD interprets data you provide (and how it cannot show what it
doesn't know, since you didn't tell VMD about it).

did you tell VMD what bonds you created? probably not? so it guessed,
and it guessed wrong since it doesn't know anything about what your
coordinate data represents. just that you have two atom types.

so you have to blame yourself for not providing sufficient information to VMD.

axel.

2

Hi, thanks for the guidance.

Yes, I think I didn’t give enough information to VMD after looking into it.

I use the moltemplate to generate the input data information and visualize by using VMD, no extra bond
But after relaxing the system and visualize the dump file by VMD, it gives extra bond.

I also look the data file generated by moltemplate and dump file by LAMMPS, they are different.

I followed this post http://lammps.sandia.gov/threads/msg08288.html, but still couldn’t solve the problem.

Could you give me hits?

Best Wishes!

3

Hi, thanks for the guidance.

Yes, I think I didn't give enough information to VMD after looking into it.

I use the moltemplate to generate the input data information and visualize
by using VMD, no extra bond
But after relaxing the system and visualize the dump file by VMD, it gives
extra bond.

I also look the data file generated by moltemplate and dump file by LAMMPS,
they are different.

I followed this post http://lammps.sandia.gov/threads/msg08288.html, but
still couldn't solve the problem.

topotools is the way to go. if it doesn't work for you, you likely
didn't use it correctly. docs are here:
https://sites.google.com/site/akohlmey/software/topotools/

axel.

4

Hi, thanks for the information.

Finally, my problem solved.

You are right, I didn’t use it correctly.

Best Wishes!