I want to study the interaction of non covalent interaction of amino acid and naphthalene.
The question lacks some important information, so I'm not sure what is it exactly that you want to study. Is it just one amino acid molecule interacting with one naphtalene molecule via van der Waals forces? If so, the system is small enough to employ DFT (with a functional than can well describe non-covalent interactions, e.g. m06 class) or even MP2 methods. Just optimize the geometries of the amino acid and napthalene separately and then together (try starting from different starting geometries, there may be several local minima) + do couterpoise calculations to get a very accurate interaction energy.
If you need a bulk system with a larger number of molecules - CHARMM force field (implemented in charmm, namd and so on) should give reasonable description of such non-covalent interactions.
Thank you for reply. Actually i want to study the orientation of aminoacids on napthalene, coronene and graphene. since aminoacids has many active sites DFT calculation lacks in giving multiple minimas. Is there any way by which i can get all possible minima on interaction of aminoacid with graphene.
You could try to use OPLS-AA parameters and the DL_POLY program version 2. However, the optimization procedure of DL_POLY is not perfectly suited for finding ALL minimas. Constructing a specific force field for your application from ab initio calculations would also be a possibility if you need higher accuracy.
try ReaxFF from potentials A. van Duin (simply googlize ReaxFF) and use LAMMPS for running MD.
There's many alternative of molecular dynamics simulation, NAMD, CharmM, gromacs, ecc. But you need to know exactly your goal before choosing software. If you are interested i recently pubblished same papers dealing interaction of PAH with Proteins
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