Dear all,
I am trying to make a “long” polymer nanofiber.
First, I built “short” polymer nanofiber and equilibrated it.
After that I created a “long” structure by using the created “short” structure with topotool in VMD.
By the way, during the equilibration by using “fix nvt”(equilibration stage2) for the “long” structure, atoms keep blowing up.
I would really appreciate it if anyone could explain this phenomenon.
Attached is the data file for Lammps input.
My code is as follows;
data.fiber_long (753 KB)
Dear all,
I am trying to make a "long" polymer nanofiber.
First, I built "short" polymer nanofiber and equilibrated it.
After that I created a "long" structure by using the created "short"
structure with topotool in VMD.
By the way, during the equilibration by using "fix nvt"(equilibration
stage2) for the "long" structure, atoms keep blowing up.
I would really appreciate it if anyone could explain this phenomenon.
have you visualized the structure?
your bonds seem _completely_ messed up.
that would easily explain the "blowing up"
axel.
Dear Dr. Kohlmeyer,
I have visualized the structure.
Atoms stay still with a little vibration during the equilibration stage1.
But during the equilibration stage2 with nvt, they begin to blow up.
This must be a stupid question but how did you find out that my bonds are completely messed up?
How do you judge that?
Can I fix my messy bonds? Or do I have to rebuild my initial structure?
If I can fix my messy bonds, could you give me any suggestion for that?
Thank you for your help and I really appreciate it.
Justin
Dear Dr. Kohlmeyer,
I have visualized the structure.
Atoms stay still with a little vibration during the equilibration stage1.
But during the equilibration stage2 with nvt, they begin to blow up.
This must be a stupid question but how did you find out that my bonds are
completely messed up?
i read in your data file into VMD with topotools.
How do you judge that?
it is _very_ evident from looking at the input.
Can I fix my messy bonds? Or do I have to rebuild my initial structure?
i don't know. it depends on how you built your system altogether.
axel.