Decomposition analysis

[Reza Khayat]

Hi,

How are the amino acids selected for decomposition analysis? Are they selected from the first frame, the last frame, or for every frame analyzed? I have a system where two subunits slide across one another during the simulation. Consequently, if two amino acids are far apart at beginning and end of simulation but close to one another in the middle, will their interaction be identified? Thanks.

Best wishes,

Reza

[Mario Sergio Valdes]

The residues are determined from the first frame. This means that you will not be able to compute the contribution of residues that are initially farther away than the selected cutoff. However, you can specify which residues select. You can analyze your trajectory, determine the residues of interest and define them explicitly in the print_res variable. Please refer to how to define individual residues and ranges here.
Note that the bar chart represents the average over the trajectory. This means the result may not be accurate if the interaction changes considerably along the trajectory. However, such information is shown in line graphs for each selected residue.
HTH!

[Mario Ernesto]

The amino acids are selected from the first frame. That way, in your system you will probably need to run the calculations for single frames using scripting eg. Python or bash 

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[Reza Khayat]

Thank you both!