Dear lammps-users,
How to increase the number of atoms for Alanine amino acid.
Thanks
Dear lammps-users,
How to increase the number of atoms for Alanine amino acid.
how does this question relate to LAMMPS?
also, alanine is a molecule with a specific molecular structure. if you add
atoms to it, it will no longer be alanine.
axel.
Excuse me, I started to use yet lammps. I am trying alanine molecule (not in the mebran, simple alanine molecule) on Lammps. I want to ask. Without changing the structure of the alanine molecule,want to increase the number of molecules. So I want to increase the number of same alanine molecule. I wonder if this is possible?
Yes, check out the molecule command (http://lammps.sandia.gov/doc/molecule.html) and create_atoms command (http://lammps.sandia.gov/doc/create_atoms.html).
Ray
Excuse me, I started to use yet lammps. I am trying alanine molecule (not
in the mebran, simple alanine molecule) on Lammps. I want to ask. Without
changing the structure of the alanine molecule,want to increase the number
of molecules. So I want to increase the number of same alanine molecule. I
wonder if this is possible?
it seems to me, that you are not only new to LAMMPS but to MD simulations
in general. you should talk to your adviser and get proper instructions and
tutoring. neither the LAMMPS manual, nor posting questions on this mailing
list will be sufficient to acquire the necessary skills and experience, and
even if you manage, you will likely waste a *lot* of time (yours primarily,
but also that of others).
there are many ways to do what you ask for. you can use external tools
used to set up molecular geometries to build a larger system (graphical
molecule editors or tools like packmol). there are also tools like
moltemplate (bundled with LAMMPS) that can be used to build larger/complex
systems. also the topotools plugin for VMD has a LAMMPS backend and an
option to replicate molecules/systems.
ray already mentioned the "molecule" command and using it in combination
with "create_atoms". that is probably the least beginner friendly option.
if your desire is solely to replicate an existing system, then you can
simply use the "replicate" command.
axel.