MDFF News and Announcements

MDFF News and Announcements

Workshop on MDFF (Nov 2016)

MDFF will be presented during the upcoming workshop in San Francisco taking place December 12-16. An overview of the method will be given in a lecture in the morning, followed by the tutorials in the afternoon.

Workshop on MDFF (Oct 2016)

MDFF will be presented during the upcoming workshop in Urbana taking place October 17-21. An overview of the method will be given in a lecture in the morning, followed by the tutorials in the afternoon.

Timeline Correlation
made with VMD

VMD 1.9.2 Released: UPDATE (February 2015)

February UPDATE: The MDFF tutorial has now been updated to cover the latest MDFF features outlined below, including the MDFF GUI, interactive MDFF, and Timeline cross correlation analysis.

VMD 1.9.2 contains several updates for the Molecular Dynamics Flexible Fitting (MDFF) Method. The mdff plugin contains new options for setting up MDFF simulations with implicit solvent and the new MDFF method for low-resolution x-ray crystallography (xMDFF, recently detailed in this article). Complete details for setting up xMDFF simulations with this plugin can be found in the MDFF tutorial. Additionally, a new graphical user interface for the mdff plugin is now available in the Modeling section of the Extensions menu. This interface allows for easier setup of MDFF and xMDFF simulations, as well as running, connecting to, and analyzing interactive MD simulations. VMD 1.9.2 also contains new multi-core CPU and GPU-accelerated analysis capabilities for MDFF, as described in a recent article. The mdffi cc command can be used to quickly compute the cross correlation of a structure to a target density map much faster than previous methods. This speedup allows for the analysis of very large structures (millions of atoms) and very long (microsecond range) trajectories, and at a much finer level of detail than was previously feasible. The Timeline plugin uses this new fast cross correlation method to visually present the results of the analysis, making it easier than ever to determine the quality of fit for a MDFF simulation and to quickly identify poorly fitting regions of a structure that require further simulation. More information about other latest features of VMD version 1.9.2 can be found on the release page.

Timeline Correlation
made with VMD

VMD 1.9.2 Released (December 2014)

VMD 1.9.2 contains several updates for the Molecular Dynamics Flexible Fitting (MDFF) Method. The mdff plugin contains new options for setting up MDFF simulations with implicit solvent and the new MDFF method for low-resolution x-ray crystallography (xMDFF, recently detailed in this article). Complete details for setting up xMDFF simulations with this plugin can be found in the MDFF tutorial. Additionally, a new graphical user interface for the mdff plugin is now available in the Modeling section of the Extensions menu. This interface allows for easier setup of MDFF and xMDFF simulations, as well as running, connecting to, and analyzing interactive MD simulations. VMD 1.9.2 also contains new multi-core CPU and GPU-accelerated analysis capabilities for MDFF, as described in a recent article. The mdffi cc command can be used to quickly compute the cross correlation of a structure to a target density map much faster than previous methods. This speedup allows for the analysis of very large structures (millions of atoms) and very long (microsecond range) trajectories, and at a much finer level of detail than was previously feasible. The Timeline plugin uses this new fast cross correlation method to visually present the results of the analysis, making it easier than ever to determine the quality of fit for a MDFF simulation and to quickly identify poorly fitting regions of a structure that require further simulation. More information about other latest features of VMD version 1.9.2 can be found on the release page.

Structure of HIV (May 2013)

The capsid of the human immunodeficiency virus type 1 (HIV-1), the major cause of AIDS, has recently had its full atomic structure determined. This discovery was made in part through the use of MDFF and marks the largest structure ever determined utilizing MDFF, at over 3 million atoms. This feat was made possible due to the performance and scalability of NAMD which MDFF is built into. This integration with NAMD allows MDFF to be run on a wide variety of platforms, including large supercomputers such as BlueWaters which was used for simulating the HIV capsid. In addition, due to the MD based nature of MDFF, the capsid structure could be immediately used for the additional simulations which took place after the initial fitting. More information is available in this highlight.

Funded by a grant from
the National Institute of
General Medical Sciences
of the National Institutes
of Health