Dear All,
I'm preparing a non-periodic initial micro-structure of a CG polymer.
One way it's usually done is the following:
after relaxation and equilibration at specific temperature using PBC,
all atoms are wrapped in a unit cell and those
which cross the boundary are split.
wrapping is simple with
pbc wrap -compound chain (pbc tool for VMD)
topo tools can brake bond (delbond <id1> <id2>),
but then i guess nothing happens to angle potentials which
share these two atoms.
I just wonder if anyone else had the same problem and maybe
already implemented some Tk/Tcl script for deleting bonds and
angles (I don't have dihedrals because I work in 2d at the moment).
Kind regards,
Denis
Dear All,
I'm preparing a non-periodic initial micro-structure of a CG polymer.
One way it's usually done is the following:
after relaxation and equilibration at specific temperature using PBC,
all atoms are wrapped in a unit cell and those
which cross the boundary are split.
wrapping is simple with
pbc wrap -compound chain (pbc tool for VMD)
topo tools can brake bond (delbond <id1> <id2>),
but then i guess nothing happens to angle potentials which
share these two atoms.
exactly.
totpotools commands are not supposed to make any assumptions
about your system unless explicitly stated. this is to give you
maximum flexibility.
I just wonder if anyone else had the same problem and maybe
already implemented some Tk/Tcl script for deleting bonds and
angles (I don't have dihedrals because I work in 2d at the moment).
you can just use the delangle command in topotools.
it would be fairly straightforward to add code to the delbond
command (and correspondingly to the addbond command)
to have them delete or created "bond topology dependent"
angles, dihedrals, and/or impropers. i'll have to think about
how to do this in a clean fashion for a while, though.
cheers,
axel.
Check the delete_bonds command in LAMMPS. It can
delete all interactions between atoms in a group.
Steve