Dear Lammps users,
Im wondering if I can calculate the energy and remaining/filled volume in the box in the following setup. First, I will construct two boxes where in box1 will place RNA/protein structure using pdb file and place fix number of polyethylene molecules (say 10 or some number) in box2. Now i want to transfer the RNA molecule from box1 to box2 and estimate the energy and volume of box2. I also need the energies and volumes of both boxes before any transfer which can be done using one box for both molecules one by one.
Or in otherway, i can introduce the RNA molecule at random position and orientation in only one box containing already polyethylene molecules and determine the energy and volume of box after placing RNA.
any help or idea would be great help.
looking forward to hear from you
Regards,
Sajid
Dear Lammps users,
Im wondering if I can calculate the energy and remaining/filled volume in
the box in the following setup. First, I will construct two boxes where in
box1 will place RNA/protein structure using pdb file and place fix number of
polyethylene molecules (say 10 or some number) in box2. Now i want to
the number 10 is a useless indicator. better to state the number of
carbon atoms or something equivalent that gives an impression of how
much volume those will cover.
transfer the RNA molecule from box1 to box2 and estimate the energy and
volume of box2. I also need the energies and volumes of both boxes before
what do you need those values for?
any transfer which can be done using one box for both molecules one by one.
Or in otherway, i can introduce the RNA molecule at random position and
orientation in only one box containing already polyethylene molecules and
determine the energy and volume of box after placing RNA.
any help or idea would be great help.
looking forward to hear from you
before giving any advice, you need to explain a bit more what the
overall purpose of your simulations is going to be.
it is most certainly not possible to simply place a large molecule
inside a dense system directly. there is no space, it would overlap
with existing atoms.
axel.