Hello All,
I’m using Packmol to generate initial conformations. However it does not establish good PBC. I’m needing good PBC because I’m doing deformation simulations and I’m noticing that the simulation box is fracturing at the PBC interface. I’m wondering if there is a fix (I was looking at move) of some method that could be used to establish a good PBC quickly. When looking at the simulation boxes hydrogen bonding, I notice the actual box has isotropic H-bonding density however at the PBC interface there is little H-bonding, hence why I’m getting poor fracture at the interface.
Thank you for your time.
Hello All,
I'm using Packmol to generate initial conformations. However it does not
establish good PBC. I'm needing good PBC because I'm doing deformation
simulations and I'm noticing that the simulation box is fracturing at the
PBC interface. I'm wondering if there is a fix (I was looking at move) of
some method that could be used to establish a good PBC quickly. When
no, there isn't.
looking at the simulation boxes hydrogen bonding, I notice the actual box
has isotropic H-bonding density however at the PBC interface there is little
H-bonding, hence why I'm getting poor fracture at the interface.
packmol has no idea of force fields, so you need to do a proper
equilibration anyway. the best strategy is to start from a rather
small system and then use the replicate command to build a larger
system along the periodic dimension(s). to get from an initial,
artificial structure to a reasonably equilibrated state efficiently,
usually requires a number of steps, like minimization, thermalization
(fix langevin can be very helpful for that), box adjustments (via a
barostat or something equivalent).
axel.
Axel,
Is it a bad/dumb idea to generate a specific box size in packmol, and then in lammps set the periodic conditions to be smaller than the packmol box size?
As an example, in packmol, generate a starting config with box lengths 50 and in lammps, set the periodic conditions to be 45. And slowly allow the box to relax using minimizations and NPT.
Thanks again.
Axel,
Is it a bad/dumb idea to generate a specific box size in packmol, and then
in lammps set the periodic conditions to be smaller than the packmol box
size?
yes and no. depends on how you set up your system for equilibration
and how regular or irregular a structure you want.
normally you'll get overlaps and that is bad. so you need to make
your box *larger* and then carefully shrink it. that is if you want to
have a regular system as equilibrated system. if you don't mind
something more irregular you can just let stuff overlap and start with
using the pair style "soft" and use fix adapt to 'grow' the non-bonded
(repulsive) interactions. this will smoothly resolve overlaps. once
that is done, you can switch to your regular force field.
there is no good general strategy. it always depends a lot on what you
want to do, what your force field is and how well you want your system
to be equilibrated. since equilibration is a state, it doesn't matter
how you get there, so sometimes people do rather crazy things.
As an example, in packmol, generate a starting config with box lengths 50
and in lammps, set the periodic conditions to be 45. And slowly allow the
box to relax using minimizations and NPT.
it is always smoother to go from a larger to a more compact a system
than the other way around. if you want to start with a known density,
you better run with fixed volume.
axel.