Understanding MMPBSA input file

[Sanjay Paul]

Hello everyone...

I want to calculate the binding energy of 100 frames from the last 10 nanoseconds of the trajectory. So, the time gap between the two frames should be 100 picoseconds.

As total simulation time =150 ns, the trajectory contains 15000 frames and the time gap between two frames is 10 picoseconds as default. 

if I select 1st frame = 14901

                  last frame = 15000    in the input file...total frame will be 100 hundred but it will include only the last 1 nanosecond.....!!!!

Please suggest modifications in my input file...I have attached one....plz help me to modify it.

[Mario Sergio Valdes]

Using startframe=5001 and interval=100 you performed the calculation for 100 frames for the last 100ns

[Mario Sergio Valdes]

The correct answer...

If you have used a time step of 10ps, to calculate the energy for 10 ns you must use 1000 frames, so the setting will be

startframe = 14001  ---> 15001 - 14001 = 1000 frames

interval = 10   ---> 1000 frames / 10 = 100 frames energy

Note that gmx_MMPBSA does not use time steps, but frames. It is the user's responsibility to set the appropriate number of frames. So you must compute the number of frames according to the time step you used in the simulation