NAFlex Input Options: Analysis (MD Trajectory)

If Analysis (MD Trajectory) option is chosen, a new project is created with the input trajectory as the root of the tree (base object to work with). (See Workspace)

Note that NAFlex has a limit file size of 100 MB.

Different input files are required depending on program and trajectory formats (NAMD/Amber/Gromacs). Gzipped files are accepted.

Gromacs Trajectory Input Files

Gromacs Trajectory Input Files Example

NAMD/AMBER Trajectory Input Files

NAMD/Amber Trajectory Input Files Example

NAFlex admits the compressed PCZ format, which can be very useful when uploading trajectories, because of the file size limitation of the server. Compressing an all-atom trajectory saving a 90% of the explained variance can produce a trajectory up to 200 times smaller in size than the original one, and with no significant loss of the original flexibility information. More information about PCZ format can be obtained from:

PCAZip compression

PCZ Compression of Nucleic Acid Trajectory Example