Hello, Lammps users,
I am wondering if Lammps can do the molecular mechanics modeling ? The main aim is to find the lowest energy conformation of a molecule that is equilibrium with another one.
Thank you very much,
Best wishes,
Wei
Hello, Lammps users,
I am wondering if Lammps can do the molecular mechanics modeling ? The
main aim is to find the lowest energy conformation of a molecule that is
equilibrium with another one.
please have a look at the LAMMPS online documentation.
it describes everything that LAMMPS can do.
axel.
See the minimize command.
Steve
To add a bit more to Steve's answer. The minimize command alone will
not drive you to the global minimum (GM) as it is a tool to converge
the system to a local energy minimum. You'll have to put some extra
work to find the GM. Unless you get lucky and your initial config
corresponds to a slightly distorted GM the minimize commando won't
take you there.
Carlos
To expand on this further. Minimization will always take you to the nearest local energy minimum from your input structure. To find a global energy minimum you need to do conformational searching. Within the context of Lammps that would mean running a simulation, extracting structures from the dump file and minimizing them in hopes of finding lower energy structures. Depending upon the size of your system there may be more efficient methods for conformational searching (see Gmmx in Pcmodel or Conflex). You should consult any of the standard texts on molecular modeling, such as the one by Leach, for a discussion of the many methods available for conformational searching.
Kevin