Hello everyone,
How to create data file for LAMMPS simulation when there are thousands upon thousands atoms and complicated topology stucture? This is a big question that restrict its application. Unlike Gromacs or Amber etc, LAMMPS does not possess some usefull command to create data from PDB or others. I only know to tools, amber2lmp and ch2lmp of LAMMPS for translating data.
But ,I know nothing of Charmm and Amber.
How can I obtain the data file? Is there other tools? How can I translate data and force field of Gromacs to LAMMPS?
Any suggestion is appreciated? Thanks in advance.
Hello everyone,
How to create data file for LAMMPS simulation when there are thousands
upon thousands atoms and complicated topology stucture? This is a big
question that restrict its application. Unlike Gromacs or Amber etc,
i disagree. lammps supports simulation of a very large variety of
systems, and for the most cases you will have to write a custom tool
for generating topology data anyways. the automated tools of _bio_
simulation tools _only_ work well for these kind of systems. there
is no easy way to extend those beyond those simple to handle cases,
and quite often lammps is not as efficient as those simulation packages,
which are optimized towards those setups.
LAMMPS does not possess some usefull command to create data from PDB
or others. I only know to tools, amber2lmp and ch2lmp of LAMMPS for
translating data.
But ,I know nothing of Charmm and Amber.
so learn about them. sorry, but "no pain, no gain".
How can I obtain the data file? Is there other tools? How can I
translate data and force field of Gromacs to LAMMPS?
as in all open source packages, most features are developed on a
"need-to-have" basis. so if you need a tool for this conversion,
you will have to figure it out for yourself, or motivate somebody
to do it for you (note: "i want it", is not very motivating).
most of the existing tools are there, because somebody else had
the need, implemented it, and was nice enough to share it.
that being said, i'm currently working on a package that is integrated
into VMD, that will allow to import, manipulate, and export topology
data (including LAMMPS data format files). i have been asked to consider
writing a backend to write out minimal gromacs topology files, so
that gromacs analysis tools could be used with (coarse grained)
LAMMPS generated trajectory files. you would be more than welcome
to contribute an importer module for gromacs format .top files.
cheers,
axel.