doubt with frame count in input file of mmpbsa calculation

[Divpreet kaur]

Good Morning to all. 

I was trying to run mm pbsa calculation using gmx_mmpbsa and while i have generated the input file for the same. The default value for start frame= 1 and end frame = 9999999.

I would like to ask if it is for 1000 ns trajectory? Does that mean 1 frame=1 ps??

Please let me know. I will be thankful to you.

Regards

Divpreet kaur 

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[Mario Ernesto]

those are the default values but they can be changed... if you don't change them, then the calculation will be performed using all the frames from your trajectory... you can check how many frames your trajectory has with gmx check:

gmx check -f your_traj.xtc

from there you can decide how many frames you want to use for the calculation...

hope this helps!

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[Divpreet kaur]

Hi!

I just noticed that my trajectory file has 10000 frames using this command. I have also attached a picture for your reference. 

However, when i am giving frames for calculation in mmpbsa.in (input file).

For 75ns to 100ns

Start frame will be: 7501

End frame will be 10000 or 10001    ???

please confirm this.

Also, even if I put the end frame as 11000...i am still able to calculate mmpbsa and its not showing any error. How is this possible if my file has only 10000 frames?

Please help me understand this.

I would be really thankful.

Regards

[Mario Ernesto]

Of your start frame is 7501 and your endframe is 10001 the you will perform calculation for 3000 frames... If your endframe is higher than the actual number of frames, gmx_MMPBSA internaly will use as endframe the last frame of your trajectory... That why there is no error in the calculation... 

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[Mario Sergio Valdes]

The selection of the frame range is universal and does not require concern for time units. Like GROMACS and other programs, by default, the value of the variable defining the last frame is set arbitrarily, since if your trajectory contains less, then this value is reassigned internally. If you want to calculate the last 75 ns of your trajectory, then must define startframe = 2500 and may or may not define endframe = 10000. If you then want to use time units for the analysis, then define it in the gmx_MMPBSA_ana selection dialog. There, you can define from which time to start, since you can pass the last fragment of your trajectory and gmx_MMPBSA unknown the time in which it has started. You can also define the interval, which corresponds to the original time interval used in the simulation, not the one used in the calculation. Here is an example:
input_file
startframe = 2500
endframe = 99999999
interval = 1
# 7501 frames

Frame to time convertion in gmx_MMPBSA_ana
start = 25000
interval = 10
unit = ps

This will show on the x-axis 25000 ... 100000 ps

You can use the scale of ns to make it smaller
Frame to time conversion in gmx_MMPBSA_ana
start = 25
interval = 1
unit = ns
This will display on the x-axis 25 ... 100 ns
If you change the interval in the input file it would look like this
input_file
startframe = 2500
endframe = 9999999999
interval = 2
# 3751 frames
and will be displayed on the x-axis as 25000 ... 100000 ps or 25 ... 100 ns according to the scale you have selected. Note that the time range not changes, since the only change is how many frames you selected in this range.

HTH!

Mario S.