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.

Phenix: xMDFF simulations also require the third-party Phenix software suite. Phenix information and download are available here.

MDFF plugin beta: The latest version of the VMD mdff plugin and GUI including the most recent bug fixes can be downloaded here. To use this version, unpack the downloaded file and add the following line to your .vmdrc: set auto_path [linsert $auto_path 0 /path/to/mdff] where the path corresponds to the location you unpacked the downladed file to.

An MDFF and xMDFF 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 Cascade (cMDFF) or Resolution Exchange (ReMDFF) MDFF for high-resolution cryo-EM maps:

Molecular dynamics-based model refinement and validation for sub-5Å cryo-electron microscopy maps.
Abhishek Singharoy*, Ivan Teo*, Ryan McGreevy*, John E Stone, Jianhua Zhao, and Klaus Schulten. eLife, 2016

* Equal contribution.

Please cite the following reference in any work that applied xMDFF:

xMDFF: Molecular dynamics flexible fitting of low-resolution X-Ray structures.
Ryan McGreevy*, Abhishek Singharoy*, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo, and Klaus Schulten. Acta Crystallographica, D70, 2344-2355, 2014.

* 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.

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