Hi all,
I want to perform simulations of biomolecules, but could not clearly understand that how the data file of peptide is made.
Could you please shed some light on this?
Thank you.
Sincerely,
Pinky
Hi all,
I want to perform simulations of biomolecules, but could not clearly understand that how the data file of peptide is made.
Could you please shed some light on this?
most people you some kind of script or program to create those data files.
the challenge is always to assign atom types and partial charges to atoms and then get the bond topology (bonds, angles, dihedrals, impropers) and derive force field type assignments for those. you can do this with custom scripts or scripts that build on tools that can do some of the more complex work (e.g. infer the bond topology) or - and this is what most people that do simulations of biomolecules with LAMMPS do - use some force field specific tools (e.g. from CHARMM or Amber or NAMD) and then convert the resulting coordinate/topology files to a LAMMPS data file. some of these tools are bundled with LAMMPS in the tools folder, most of that are very up-to-date, so they may not work reliably with the latest version of the corresponding force fields, in some cases there are limitations in LAMMPS as well (LAMMPS is not primarily used for biosimulations, so there is not so much support for that and not so many people contributing updates or new features). you can also look up and try out external tools:
https://lammps.sandia.gov/prepost.html
it is almost always advisable to first do simulations of suitable test systems with the “native” simulation software and learn how to correctly apply that force field before trying to translate that to LAMMPS. that will also give you a reference to compare to.
axel.