polymer structural integrity.

Dear all,

I apologise for writing to this mail-list, however, I cannot activate my vmd list even though I am subscribed to it. Therefore, I wish to ask someone who uses vmd about the following issue:

while using vmd, my polymer looks structurally intact (one non-disintegrated long polymer) but when I use gnuplot to visualise the same structure, the polymer looks disintegrated.

using lammps, i have equilibrated my polymer, and the simulation runs well after equilibration, even though some "FENE bond too long" warning appear during the first steps, and do not appear later on. Does this indicate that my polymer is disintegrating after the first steps but the simulation is still able to run, or is there something strange with gnuplot? (please see dump-file and screen-shots attached).

Thank you very much for your time.

with best wishes,


test.0 (11.6 MB)

I will only comment on the LAMMPS part of your Q.
The FENE warnings are likely OK, if the model kept running.
They only indicate one or more bonds are nearly too long.
You get an error if the bond actually becomes too long,
b/c the FENE formula has a singularitly. So apparently
none of your bonds ever reached that limit - so no bond