Hi. I am simulating gas flow in a channel
I used nvt to obtain the equilibrium configuration. But when i check my system in vmd some atoms are out of my periodic boundary conditions. So i wrap molecule coordinates by below command in Tk Console .
topo read lammpsdata system_after_nvt.data full
pbc box
pbc wrap -compound res -all
but I don’t know how can i save this new configuration???
I want to use that as a new equilibrium configuration in lammps and start my NEMD simulation ?
Hi. I am simulating gas flow in a channel
I used nvt to obtain the equilibrium configuration. But when i check my
system in vmd some atoms are out of my periodic boundary conditions. So i
wrap molecule coordinates by below command in Tk Console .
that is nonsense. with periodic boundary conditions, atoms *cannot* be
outside the box. LAMMPS will correctly consider the suitable periodic
replica as needed.
the rest is really a VMD and not a LAMMPS question.
topo read lammpsdata system_after_nvt.data full
pbc box
pbc wrap -compound res -all
but I don't know how can i save this new configuration???
how on earth could you figure out how to read the configuration and
not find the explanation for how to write it? don't you read any
documentation???
I want to use that as a new equilibrium configuration in lammps and start my
NEMD simulation ?
as mentioned above, there really is no need for this outside of
convenience for visualization. but even then your atoms will move in
and out of the principal simulation cell for your production
simulation as well.
axel.
I used nvt to obtain the equilibrium configuration. But when i check my
system in vmd some atoms are out of my periodic boundary conditions. So i
wrap molecule coordinates by below command in Tk Console .
that is nonsense. with periodic boundary conditions, atoms cannot be
outside the box. LAMMPS will correctly consider the suitable periodic
replica as needed.
Maybe you mean that atoms in the LAMMPS dump file are slightly outside
the periodic box. This is normal, b/c atoms are only wrapped back
into the periodic box on reneighboring timesteps. See the dump doc
page for more details.
Steve