Dear all,
I posted this question to the VMD mailing list a week ago but got no
answer, so I'm giving it a try here...
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 (8 GB)? How could I solve this issue?
Best regards,
Laurent
Dear all,
I posted this question to the VMD mailing list a week ago but got no
answer, so I'm giving it a try here...
sorry, but it went by me due to running the LAMMPS workshop here in trieste.
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 (8 GB)? How could I solve this issue?
not sure. is this on linux or windows and 32-bit or 64-bit?
i recall fixing some size related issues in the past. if there is a
simple way to reproduce the crash, i can try running on a machine with
much more RAM.
unless there are some constraints that you didn't tell us, i would
just create a reasonably sized equilibrated box of the electrolyte and
then use the replicate and delete_atoms commands in combination with a
spherical region to prepare that kind of system. then define a larger
spherical region to get a group of molecules and do a
minimization/quench/equilibration of this layer and then simulate the
entire system.
axel.