Interface between metadynamics and LAMMPS

Question

I am trying to create an interface between the metadynamics and the LAMMPS code. Both the codes are written in two different languages. How can I proceed to create an interface.

Thank you

Answer 1

Colvars package is required to use collective variables and various methods of sampling such as metadynamics, umbrella sampling, ABF, etc. The package can be called using the fix colvars command. However, it does not come with LAMMPS and must be installed separately.

1- Based on your OS, To install LAMMPS and Colvars, carefully follow the instructions at Build lammps.

1.1. If using cmake, use the flag -D PKG_COLVARS=yes. For make, use make lib-colvars args="-m g++-debug”. You may need to modify Makefile.serial and Makefile.mpi to include the following, for example:

CC =        clang++
CCFLAGS =   -std=c++11 -stdlib=libc++

1.2. Additional packages, such as reaxff or molecules, may also be required. See here for the appropriate flags.

2. After installing Colvars, you can use it in LAMMPS by calling fix colvars. Colvars provides well-written manuals for different MD packages, including LAMMPS. Find the manual for LAMMPS here. From the manual (P. 75), to perform metadynamics, a colvar must be defined, for example:

colvar {
  name r
  distance { ... }
  upperBoundary 15.0
  width 0.2
}
metadynamics {
  name meta_r
  colvars r
  hillWeight 0.001
  hillWidth 2.0
}
harmonicWalls {
  name wall_r
  colvars r
  upperWalls 13.0
  upperWallConstant 2.0
}

3. The core functionality of Colvars is consistent across different MD packages. For questions related to Colvars, the NAMD Mailing List is a good resource.