This page gives pointers to
GUI and Analysis Software - 3rd-party software that wraps LAMMPS
Molecular Builders - software to build molecular inputs for LAMMPS
Speaking for the LAMMPS developers, we think this kind of tools, whether free-ware or commercial software, can be very useful. They extend the scope of problems that LAMMPS can model and its ease of use. We are happy to "advertise" such tools here, so that people can try them out. Send us an email if you want to add your software or tools you use to the list.
This section describes commercial software that wraps LAMMPS to provide a user-friendly environment for developing simulations models, running simulations, and analyzing the results.
The company Scienomics has created an interface to LAMMPS as part of their Materials and Processes Simulations (MAPS) platform. It can be used to visualize and perform analysis on the output of LAMMPS simulations. They also have a tool called Amorphous Builder which can be used to create input geometries for LAMMPS, plus tools to predict elastic properties and analyze the results of ReaxFF simulations. See the Scienomics WWW page for more details on all the tools.
The company Scifes Inc. has launched a software product called "Lammpsfe", which stands for LAMMPS frontend, which is a user interface specifically created for LAMMPS. Lammpsfe consists of a GUI for creating LAMMPS input scripts and an MDViewer for LAMMPS output visualization. It runs on Linux,Mac,Windows. The MDViewer, which is based on the latest OpenGL-technology, includes such capabilities as viewing several millions of atoms as well as looking at LAMMPS trajectories with changing numbers of atoms/molecules.
To simulate molecular systems LAMMPS requires you to input molecular topologies (lists of bonds, angles, dihedrals, etc) as well as force-field coefficients appropriate for your model. Thus the task of building a molecular system is a pre-processing step, and can be a complex task of its own.
This section describes tools that help to automate this process.
Generally speaking, the packages can infer angle, dihedral, and improper interactions from bond topology. They have commands to generate molecular geometry. They can read coordinates from files generated by PACKMOL and other PDB file builders.
Developed and maintained by Andrew Jewett (UCSB), jewett.aij at gmail.com.
This tool is distributed with LAMMPS in the tools/moltemplate directory. See that directory and the moltemplate home page for more details.
Moltemplate was designed for building coarse-grained biomolecular models. Moltemplate can create both: lammps DATA files (containing geometry and topology), and lammps INPUT scripts (containing force-fields, fixes, and groups). Unlike files generated by other conversion tools, moltemplate gives users access to all of the force-fields available in LAMMPS. Users can save molecules in moltemplate's compact, readable template file format (".LT"), and share them with others. Molecules can be used as building blocks for bigger molecules. "Canned" force-fields (such as Dreiding, GAFF, TraPPE, and user creations) can (in principle) also be saved in this format and applied to molecules later.
Molecules can be copied, combined, and linked together to define new molecules. (These can be used to define larger molecules. Unlimited levels of object composition, nesting, and inheritance are supported.) Once built, individual molecules and subunits can be customized (atoms and bonds, and subunits can be moved, deleted and replaced).
Here are examples of systems built with moltemplate. Click on them for a larger image.
Developed and maintained by Axel Kohlmeyer (Temple U), akohlmey at gmail.com.
See the TopoTools home page for more details.
Topotools is a molecule builder which leverages the power of VMD and TCL to create lammps DATA files and convert them to and from other formats. Topotools has two components: a middleware script which can extract and manipulate topology information, and several high-level applications built on top of it, which, for example can enable it to read/write data files, replicate and merge systems. Together with VMD, topotools can infer topology from PDB files, PSF files, and atom pair distances, solvate a protein. Additional features for coarse-grained molecules are planned.
Need to add some pictures.
Developed and maintained as an open-source project.
See the Avogadro home page for more details.
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.