Hello,
I am trying to study the interaction of graphene with a polymer.
I am trying to generate a periodic molecule of graphene that bonds to itself even beyond the pbc box. Right now, I am using boundary command in my LAMMPS script and I am getting discrete sheets of graphene when I view the periodic images in X and Y directions in VMD.
A similar command on GROMACS, to what I am looking for, is the periodic-molecules. (Search in the link given below)
http://manual.gromacs.org/online/mdp_opt.html
Any help in this regard would be truly appreciated. Thank you.
Regards,
L Madhavkrishnan
BITS Pilani Hyderabad Campus
Hello,
I am trying to study the interaction of graphene with a polymer.
I am trying to generate a periodic molecule of graphene that bonds to itself
even beyond the pbc box. Right now, I am using boundary command in my LAMMPS
script and I am getting discrete sheets of graphene when I view the periodic
images in X and Y directions in VMD.
A similar command on GROMACS, to what I am looking for, is the
periodic-molecules. (Search in the link given below)
http://manual.gromacs.org/online/mdp_opt.html
you are confusing and mixing up multiple things here that are unrelated.
- first off, periodic display in VMD will *never* show you the bonds
across periodic boundaries, since it simply replicates the
non-periodic representation. if you *had* explicit bonds across
periodic boundaries, it would look in VMD as if you had bonds passing
through the entire box.
- second, that gromacs option you are referring to, does not do what
you say it does. it merely changes how gromacs stores coordinates of
molecules so that they are output as whole molecules. turning this on
or off has no impact on the bonding. LAMMPS doesn't require this since
it stores periodic image counters with each atom and does not apply
minimum image conventions. thus it has no performance impact and you
can at any time whether you want to store unwrapped or wrapped
coordinates in your trajectory file
- third, if you use a potential with implicit bonds for your graphene,
LAMMPS will consider the bonds across periodic boundaries
automatically as *all* bonds will be computed implicitly during the
non-bonded calculation. if you use a potential with explicit bonds,
you will have to provide the bond information in the data file
explicitly (LAMMPS will warn about inconsistent image flags in this
case, but will correctly consider the closest image for the bond, if
the rest of the input is correct and consistent with it).
so you don't need another input option, but you do have to provide the
correct input to get the simulation you want.
axel.
Thank you for the reply.
I would like to generate a graphene sheet that is infintely long and simulate the interaction of a polymer with the same. I have tried a few ways and I have only got discrete sheet simulations.
You can view my input script and data file here- https://goo.gl/hoC6TT
Can you please let me know what the problem in the file is? Also, how do I go about generating an infinite graphene sheet?
Regards,
L Madhavkrishnan
BITS Pilani Hyderabad Campus
Thank you for the reply.
I would like to generate a graphene sheet that is infintely long and
you cannot do that, as that would require an infinite number of atoms
and an infinitely large computer and a new programming language and so
on. what you want is a sheet that continues across periodic
boundaries.
simulate the interaction of a polymer with the same. I have tried a few ways
and I have only got discrete sheet simulations.
are you aware how useless such a statement is? it doesn't convey any
information outside of your lack of ability to solve a given problem.
it is really simple. there are two options: 1) if you have a potential
with implicit bonds, all you need are the positions and a suitably set
up periodic cell. 2) otherwise you need to specify all positions,
bonds, angles, dihedrals.
You can view my input script and data file here- https://goo.gl/hoC6TT
Can you please let me know what the problem in the file is?
this mailing list is not an input file correction service. in any
case, your problems seem more to be of the kind that you don't fully
understand how to set up simulation inputs for your specific needs,
and that cannot be corrected by correcting your script.
axel.