Vmd topotools how to#
Vmd topotools manual#
Vmd topotools software#

However they still have the freedom to easily customize individual interactions when needed.ġ.1 Converting LT files to LAMMPS input/data files (With help, more popular force-fields can be converted.) This way moltemplate users can build a molecule by specifying only a list of atoms in the molecule and the bonds connecting them.

Popular force-fields such as AMBER GAFF and OPLS-AA have been converted into LT format, allowing users to quickly create molecules using moltemplate. (These molecules can be used to build even larger molecules.) Once built, individual molecules and subunits can be customized (atoms and bonds, and subunits can be inserted, moved, deleted and/or replaced). Moltemplate can then duplicate the molecule, customize it, and use it as a building-block for constructing larger, more complex molecules. LT files are templates containing all of the text relevant to a particular molecule (including coordinates, bond-topology, angles, force-field parameters, constraints, groups and fixes). (See section 2.)Ī simple file format has been created to store molecule definitions and force-fields (the LAMMPS-template format, LT). Downloading these examples is highly recommended.

Vmd topotools how to#

However numerous examples and README files are available to demonstrate how to run these kinds of simulations.

Vmd topotools manual#

Warning: This manual does not explain how to run “active-matter' simulations or use all-atom force fields. Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology.Moltemplate Manual-(1)(Andrew Jewett, Jensen Lab (Caltech), Shea Lab (UCSB))

Vmd topotools software#

These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.īy applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. This article is cited by 32 publications.