VMD-L Mailing List

From: Laurent Joly (ljoly.ulyon_at_gmail.com)
Date: Sun Mar 23 2014 - 18:11:29 CDT

Dear all,

I am trying to build a system consisting of a bubble in an aqueous
electrolyte. I generate a pdb file using packmol, and I then convert
it to a lammps data file using the VMD Topotool plugin:

topo retypebonds
topo guessangles
topo writelammpsdata data0

For small bubbles (and small simulation boxes) everything works fine,
but above a certain system size vmd crashes (my last try was with a
little bit more than 500'000 atoms, but it crashed even for smaller
systems). Could it be related to the small amount of memory on my
laptop? How could I solve this issue?

Best regards,
Laurent