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Go-ModelWithReplicaEx

To run the GO Model Version of LAMMPS with Replica Exchange, you will need the files in this tar file.
Two types of files are contained in this archive: 1) C++ source files that are to be added to LAMMPS, 2) sample input files for an antibody to run LAMMPS, and 3) Scripts for compiling and submitting a job.

Description of the .tar contents

  • GO_1igt.in Sample LAMMPS input script (for Antibody)
  • GO_1igt.data Sample LAMMPS data file (for Antibody)
  • GO_1igt_native_contacts.mod Sample LAMMPS modification 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 to implement the Karanocolas and Brooks Go Model for proteins.
  • quick.sh Sample submission script to run a simulation on the BYU Supercomputer.
(If you are doing replica exchange, you need to make sure the number of partitions and processors are synced with what is in GO_1igt.in)
  • Makefile.mpi_go This is the makefile used for Replica exchange, Go-model compiling.

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-replica to include package for replica exchange
  • 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