This effort comprises Specific Aims 1 and 4 of Project IV of the resource. Widely-used simulation programs like Amber and CHARMM have the capability to use """"""""off-lattice"""""""" and """"""""reduced"""""""" potential models like the ones being developed in this resource, but are rarely used for this purpose because suitable library files and documentation are not readily available. This subproject has the goal of developing these libraries, along with detailed examples and tutorials, so that we can leverage the experience that many have in using these programs, and can also leverage the extensive work done in these programs for parallel molecular dynamics simulations. During the past year, we have taken steps toward this end by working to rationalize the CHARMM and Amber input formats and to create filters to allow force field and topology files defined for one of the platforms to be converted to the other. This effort (assisted by Tom Cheatham at NIH and Dennis Sprous at Wesleyan University) is now nearing completion, with Amber force fields running in CHARMM and vice-versa. Furthermore, we have been working to make the long-range electrostatic behavior (under the particle-mesh Ewald option) more consistent in CHARMM and Amber. This has now been accomplished, with the result that both energies and forces are now identical in the two codes when PME is turned on and the Amber force field is used. Completion of the same task when the CHARMM force field is used is expected shortly. This requires programming a new functional form for improper torsions into the Amber codes. Preliminary work along these lines has been carried out, and we expect no key obstacles to completion. So far, the efforts described in the above paragraphs deal with all-atom models for biomolecules, but the progress made so far will be key in extending the ideas to reduced models as well. The file format conversions and exact energy reproductions in the two codes at the all-atom level will facilitate conversion of reduced model libraries between the CHARMM and Amber environments. As discussed in another subproject description, substantial progress has already been made in converting reduced representation files from yammp to Amber, and completion of this connection will be a primary goal for the coming year.
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