Any suggestions for a good and relieble software package (free or commercial, graphical or command line) that can do the following:
1)Molecular docking on graphite, tubes, metals .... etc to simulate adsorption and desorption
2) Molecular dynamics
3) MMPBSA
4) Simple DFT calculations on Docked poses
5) Studies of surface tension and orientation at surfaces
LAMMPS and GROMACS are one of the softwares which carry out molecular dynamics, however these are based on the classical mechanics in which fundamental particles like atoms and molecules are modeled as hard spheres interacting with each other with a suitable force-field. In classical mechanics you cannot carry out DFT calculations as those are based on Quantum mechanics.
For DFT, you have to solve the Schrodinger's equation, which is not possible with LAMMPS. For that, you can use VASP software which computes an approximate solution to the many-body Schrödinger equation.
You can find these softwares online.
No matter what you do in the end you will need to tie multiple programs together:
Commercially: Schrodinger has suite that will do just everything you're asking from a Gui - but using the CLI is a pain (its not set up with a CLI user I mind).
ICM and several others are out there as well.
For open/academic licensed you'll have to figure out yourown set:
I'd recommend starting by looking and either the QM side or the MM/MD side then look at what other options play nice.
Coming from a protein perspective, Gromacs is my first goto for MD/MM stuff http://www.gromacs.org/Documentation/How-tos/QMMM , and from folks working with smaller systems LAMMPS remains well like, AMBER is very popular with the NMR folks I know, but if you love thermo there is Chamm .... if you're going to working on a het-cluster or lots of small sims that are there is also
for QM I'm going to be lazy: https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software
for both MD/MM and docking (for which there are 2 to10x more than even listed on wikipedia) A word of warning: in many cases behind testing and parameterization is a presumption of a biological context: Take a look at close look any MD/MM forcefields
or docking programs before using them.
Coming from a Biochem
