Dear All,
Wishing you a very happy new year and properous life…
I am trying to model and understand the interaction (in LAMMPs and through visualisation tools like VMD) of at the protein surface with water molecules, particularly response of the different amino acids (hydrophobic and hydrophillic) in the presence of water molecules and to see how water molecules penetrate into protein through surface caviities.
Please suggest …
Your question is too vague. You need to read
papers about how people have done this with MD,
then figure out how to do it in LAMMPS.
Steve
Older programs like GROMACS, NAMD, AMBER, and CHARMM might be a better
fit for your needs. These programs were really designed for the
purpose of putting biomolecules in a box of water (and arguably, only
that). Currently they are also a bit faster than LAMMPS (for this
purpose). These programs come with utilities to clean up messy PDB
files, supply missing hydrogen atoms, solvate biomolecules, select
from many different canned force-fields, and analyze protein/dna
conformations, LAMMPS does not. There are also many as tutorials for
simulating proteins with these programs. Depending on what you are
doing, you might have to write your own scripts to track the position
of water molecules yourself.
If you have already built input files for AMBER, NAMD, or CHARMM. and
for some reason, you want to use LAMMPS instead, then there are
converters such as amber2lmp and ch2lmp, but I don't know whether the
authors of these scripts are still supporting them. See:
http://lammps.sandia.gov/doc/Section_tools.html
However, if you want to represent the surface of your protein using a
simpler surface, or using a coarse-grained representation, then LAMMPS
might be a very good choice.
I hope this helps.
Cheers
Andrew