ComplingGo-Model
To run the GO Model Version of LAMMPS, you will need the files in this tar file. Two types of files are contained in this archive: 1) files that are added to LAMMPS, 2) sample input files for an antibody to run LAMMPS, and 3) a shell script for submitting a job to the BYU Supercomputer. The latter can be used as an example if desired.
Description of the Files
GO_1igt.in The LAMMPS input script (for Antibody)
GO_1igt.data The LAMMPS data file (for Antibody)
GO_1igt_native_contacts.mod The LAMMPS input file that contains a list of the native contact (for Antibody)
pair_lj_cut_eten.cpp and pair_lj_cut_eten.h C++ files that are added to the LAMMPS source code when compiled to implement the Karanocolas and Brooks Go Model for proteins.
quick.sh The submission script to run a simulation on the BYU Supercomputer.
Compiling on the BYU Supercomputer
- Follow the standard steps to download LAMMPS (described on the LAMMPS website)
- Copy pair_lj_cut_eten.cpp and pair_lj_cut_eten.h into the src/ directory in LAMMPS
- Copy Makefile.mpi_go into the src/MAKE/ directory in LAMMPS
- Go to the src/ directory in LAMMPS
- Type make clean-all
- Type make yes-rigid to include the SHAKE package
- Type make yes-molecule to include package for site types
- Type make -j 16 mpi_go
- Copy the new LAMMPS executable into your ~/bin directory
- You may have to add your ~/bin directory to your path. If so:
- ---Use the command export PATH=$PATH:$HOME/bin to add it for this session
- ---Add the above line to ~/.bash_profile so that it will add this folder to your path every time you log in (you may have to create ~/.bash_profile)
To run the simulation
- Copy GO_1igt.in, GO_1igt.data, GO_1igt_native_contacts.mod and quick.sh to a folder where you want to run the simulations
- type sbatch quick.sh to submit the simulation to run on the supercomputer
Who do I talk to?
- If you need help you can email Anthony Gillespie at anthonycgillespie@gmail.com