Dear,
This is very essential to ask you that is this possible to form a cluster by H2O and CO or CO2 and further simulate using the NPT
ensembles by different force field like lennard-jones potential. More specifically I have attached a paper related to molecular dynamics
have been done by CHARMM. Please tell me whether this type of job can be done using LAMMPS. If possible
then tell me which section/part of the manual will be good for me to perform this kind of Job get a result like this.
Hoping better from you soon.
LAMMPS has a LJ potential (pair_style lj/cut)
and can do NPT (fix npt). If you can build your
initial system (H2O and CO and CO2 molecules
in a box), you can likely model it with LAMMPS.
LAMMPS does hot have a "builder" capability,
but several pre-processing tools can be used with
it. See lammps.sandia.gov/prepost.html.
Rajdeep,
If you don't mind learning more than the bare minimum you need to get
your task done here is another approach.
You could use the towhee code (available for free at http://towhee.sourceforge.net/) to build and equilibrate your
molecules using configurational bias monte carlo. The nice thing about
towhee is that all you need to provide in the input file related to
the atomic configuration is the type of atoms that you have, some
basic connectivity between the atoms and the force field (FF) to be
employed in the simulations. Towhee will take care of building the
molecules and assigning the proper interaction coefficients. Note that
charmm is one of the FF supported by towhee. You could then
equilibrate the system in towhee or just use the towhee capability to
create/export data input files for lammps.
Of course your towhee related questions cannot be posted here.
Carlos