Dear Users
I want to simulate DNA+Graphene+water (Nanopore DNA Sequencing). I can make Graphene and model water and also I have PDB files for DNA. But I do not know how can I add DNA to the simulation and how to complete input file and make PSF files.
Please help me kindly.
If it helps, most of the LAMMPS-specific tools for building data files
are listed on these two web pages:
http://lammps.sandia.gov/prepost.html
http://lammps.sandia.gov/doc/Section_tools.html
Setting up all-atom protein or nucleic acid simulations is an art unto
itself. There are a huge number of force-field parameters for these
kinds of simulations, and people are always arguing about which
force-field works the best for different kinds of biopolymers.
Suppose you downloaded a PDB file somewhere, you need to add missing
hydrogen atoms, fix numbering problems, resolve atom type-name
incompatibilities (there are multiple atom-type-naming conventions),
deal with non-standard residues, generate partial charges, and add
counter-ions in the surrounding solvent... LAMMPS does not come with
tools to take care of these details.
Have you figured out what kind of force-field you want to use to
handle the nucleic acids? Do you have any non-standard residues? I
think the choice of tool you use will depend on these kinds of issues.
It's true that people sometimes use LAMMPS to simulate nucleic acids:
http://lammps.sandia.gov/papers.html
http://lammps.sandia.gov/abstracts/abstract.1654.html
http://lammps.sandia.gov/abstracts/abstract.2249.html
In fact other MD software (eg AMBER, GROMACS, NAMD, CHARMM, OpenMM)
come with tools which are easier to use to help set these kinds of
simulations up. And I suspect that most people who run all-atom
biopolymer simulations in LAMMPS build these systems using those
tools. Then, they use one of the tools below to convert the files for
those programs into LAMMPS format:
http://lammps.sandia.gov/doc/Section_tools.html
If somebody has a better way to do this, please post a reply!
Cheers!
Andrew
P.S. More grumbling on this topic:
http://ehc.ac/p/lammps/mailman/message/32132731/
http://lammps.sandia.gov/threads/msg30872.html
Dear Users
I want to simulate DNA+Graphene+water (Nanopore DNA Sequencing). I can make
Graphene and model water and also I have PDB files for DNA. But I do not
know how can I add DNA to the simulation and how to complete input file and
make PSF files.
i second andrew's recommendation and have one on my own.
please first go and learn how to do simulations with DNA in water (no
graphene) *correctly* with a toolchain as it is provided by NAMD,
Amber, CHARMM, Gromacs etc. that alone will easily take a couple of
months (note: getting an input that produces a running simulation is
easy, getting such a simulation to produce correct results is the hard
part). then, and *only* then, come back and try the same in LAMMPS and
validate the LAMMPS runs against those simulations. and finally, you
can start thinking about doing DNA, graphene, water together. any
other approach, however tempting, will lead to trouble.
Please help me kindly.
please first go and learn more about force fields and how they work.
axel.