# -------- REQUIREMENTS: --------- # 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") # http://lammps.sandia.gov/doc/Section_start.html#start_3 # 2) It also may require additional features and bug fixes for LAMMPS. # be sure to download and copy the "additional_lammps_code" from # http://moltemplate.org (upper-left corner menu) # 3) Unpack it # 4) copy the .cpp and .h files to the src folding of your lammps installation. # 5) Compile LAMMPS. This is an example of a very simple coarse-grained protein. This example contains a 1-bead (C-alpha model) representation of the "unfrustrated" 4-helix bundle model used in this paper: G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) In this model, there are three atom-types (bead-types), H, L, and N representing one amino-acid each. The "H" beads represent the hydrophobic amino acids, and are attracted to eachother with a strength of "1.0" (in dimensionless units of "epsilon"). The "L" and "N" atoms are hydrophilic and purely repulsive, and only differ in their secondary-structure propensity (ie their dihedral parameters). The dihedral-interaction is bi-stable with two deep local minima (corresponding to helix-like and sheet-like secondary structure). You can adjust the bias in favor of one minima or another by modifying the angle-shift parameter in the appropriate "dihedral_coeff" command in the other .lt file. A definition for the 4-sheet beta-barell protein model is also included. If you want to simulate that molecule instead, then edit the "system.lt" file (in the "moltemplate_files" subdirectory), and replace this line: prot = new 4HelixBundle with prot = new 4SheetBundle ------------- Instructions on how to build LAMMPS input files and run a short simulation are provided in other README files. step 1) README_setup.sh step2) README_run.sh