Molecular Dynamics Flexible Fitting
Software
VMD: Setup and analysis of MDFF simulations are performed with VMD. MDFF support is available in the VMD version 1.9 or later. Currently available for Linux, Mac, and Solaris.
NAMD: MDFF simulations are performed with NAMD. MDFF support is available in NAMD version 2.7 or later.
An MDFF tutorial is available here.
Support: Please send questions related to MDFF to the VMD mailing list. For help with running NAMD, please use the NAMD mailing list.
Please cite the following reference in any work that applied MDFF:
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
Leonardo G. Trabuco*, Elizabeth Villa*, Kakoli
Mitra, Joachim Frank, and Klaus Schulten.
Structure, 16, 673-683, 2008.
* Equal contribution.
Please cite the following reference in any work that applied symmetry-restrained MDFF:
Symmetry-restrained flexible fitting for symmetric EM maps.
Kwok-Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor Sewell, and Klaus Schulten.
Structure, 19, 1211-1218, 2011.
