Other Code

Other code

Some random programs and scripts I use are posted here if I think they might be useful to someone else running polymer simulations. For some of these programs, documentation is poorly written. If you need more explanation or help using one of these programs, email

. (If I am too busy, I will say so.)

(Some of these programs have little to do with LAMMPS or moltemplate.)

genpoly_lt.py A program for generating moltemplate files that define polymers. (Usage example here.) These polymers can contain any sequence of monomers (which are moltemplate objects), use any force field, and may have one or more backbone bonds and share any number of bonds, angles, dihedrals and impropers between successive monomers. The shape of the polymer(s) can follow any curve set by the user. (This script was intended to be useful for generating extremely long polymers that would otherwise have trouble fitting within the simulation box boundaries. This program is currently included with moltemplate.)
interpolate_curve.py This program reads a 3-column text file containing xyz coordinates located along a (user-specified) curve, and interpolates them at evenly-spaced intervals. It (along with "ndmansfield") is useful prepare simulations of polymers (or polymer melts) using moltemplate. (In the past, this program was named "interpolate_mt.py". This program is now included with moltemplate.)
dlpdb is a collection of scripts for automatically downloading large numbers PDB files and extracting angles, distances, and sequences from them. It has been to measure the local structure (angles and distances) between atoms in proteins, single and double-stranded DNA exhaustively over the entire PDB library. It can be used to generate local bond-angle and dihedral-angle statistics needed for building coarse-grained models of proteins or nucleic acids. (The user has the option to restrict the statistics to atoms near the centers of helices and sheets.) There is a central README file, as well as other README files scattered throughout the archive explaining what each script does. (This code was used in Bellesia et al. Prot.Sci.,19:141-154,2010.)
gen_all_angles_topo.sh This script was intended to be invoked on the fly at regular intervals during a LAMMPS simulation in which bonds are created and destroyed automatically over time. (IE, using fix bond/create or fix bond/break. This script can automatically generate bonded 3 and 4-body angle interactions in a LAMMPS data file which contains only atoms and bonds. (Updated 2014-12-27.) This script can recalculate all "Angles", "Dihedrals", and "Impropers" in the data file, according to the atom and bond types and the current bond network. (See README file.) See README file for an example. WARNING: This script is old and may no longer work. Please report any problems. NOTE: This script requires that moltemplate is installed.)
ndmansfield A program to generate long random compact self-avoiding walks (polymer conformations) on a lattice, in an arbitrary number of dimensions (usually 3). This program provides a way to generate random curves to supply to genpoly_lt.py to prepare polymer simulations for moltemplate. (However the curves typically must be smoothed beforehand, using interpolate_curve.py , for example.) This provides one way to prepare simulations of randomly oriented polymers (or polymer melts) for use with moltemplate. (To obtain a reasistic polymer melt structure, the conformations of these polymers will need to be relaxed beforehand, typically by running a LAMMPS simulation using pair_style lj/cut/soft to allow the polymers to pass through each other.) The curve-generation algorithm is explained in Mansfield, J. Chem Phys 125:154103 (2006).