News and Notes

Sep. 22, 2011: The CHARMM release of the distribution version c36b1 on August 15, 2011 makes the re-factored and modernized Fortran 95 version of CHARMM available. The unmatched scope of CHARMM functionality remains, but the program has a significantly sleeker profile for the memory footprint, which has been reduced by a factor of ten. The latest CHARMM release contains many “under the hood” changes that will be transparent to new and established CHARMM users. However, a key functional feature is that CHARMM is now run-time size configurable, thus allowing users to tailor the size of their executable to meet the needs of their specific problem at run-time. Another aspect of the modernization is that it simplifies preparation of future releases of CHARMM with significant performance enhancements for both serial and parallel calculations as well as with graphics processor units (GPUs). For more information see this page .

Sep. 22, 2011: With recent code optimizations, including efficient lookup tables for non-bonded interactions (J Comp Chem 30: 1490-1498), molecular dynamics simulations run as fast with CHARMM as with other highly optimized biomolecular MD codes. For example, simulation of the protein NFKB solvated in explicit water (68000 atoms) on a single core requires 0.98s/step with CHARMM compared to 1.2s/step with GROMACS (JCC 30:1490), and simulation of a periodic box of 28005 TIP3P water molecules on 12 cores requires 0.12s/step with CHARMM compared to 0.15s/step with NAMD. For more information, please see this page.

Aug. 2, 2011: CGenFF is a force field for a wide range of drug-like organic molecules designed to be compatible with the all-atom additive CHARMM biomolecular force field. CGenFF was developed by specifically optimizing parameters for a wide range of organic molecules using the same methodology used for the remainder of the CHARMM additive force field (JPCB, 102: 3586 1998; JCC 21: 86-104, 2000), creating a palette of molecular fragments that may be used to build a wide range of drug-like molecules. Example molecules to which CGenFF has been applied are shown below. To facilitate the use of CGenFF an automated charge and parameter assignment server, ParamChem (www.paramchem.org) has been implemented.

The reference for CGenFF is: Vanommeslaeghe, K. Hatcher, E., Acharya, C., Kundu, S. Zhong, S., Shim, J., E. Darian, E., Guvench, O., Lopes, P., Vorobyov, I., MacKerell, A.D., Jr., “CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.” Journal of Computational Chemistry, 31: 671-90, 2010, NIHMSID 196732, PMC2888302

Jul. 11, 2011: CHARMM.org has been moved to a new web server. Please contact Tim Miller if you notice any broken links, out of date information, or bugs.

Nov. 21, 2007: The resdesigned CHARMM.org Web site is now live! If anyone has questions/concerns please address them to either Tim Miller (btmiller -at- nhlbi -dot- nih -dot- gov) and/or Youngdo Won (won -at- hanyang -dot- ac -dot- kr).