startframe endframe inputs

[jiquiambao]

Good day!

I have another question about the input parameters in the .in file. Say I have finished simulating my system and am carrying out free energy calculations, are the startframe and endframe parameters given in the examples good enough for this analysis, or would it be better if I consider the complete duration i.e., using the default settings. Are there rules of thumb in specifying startframe and endframe parameters for calculating free energies, interaction entropy, and decomposition analysis?

Thank you in advance! I appreciate your answers to my questions lately as I am new to this.

[marioe911116]

Parameters in the example files are meant to show only that gmx_MMPBSA works. Although we tried to use the input files as recommended for different calculations, some parameters have been changed to perform more expensive calculations
in a reasonable amount of time. Default parameters work fine most of the time.

Regarding startframe and endframes, usually the go-to in the field is at least 500 frames distributed throughout the simulation time (discarding the "equilibration" time). An example:

Let's say I have simulated a system for 25 ns (12,500,000 steps at 2fs/step) and I have 2500  frames (saving one frame/5000 steps). In this case, if your simulation is stable, you could discard the first 5 ns as "equilibration" time, and use the rest (20ns) of the simulation (that will be 20ns, 2000 frames). Then, the startframe will be 500 (important here, that we are talking about frames, not time), and the endframe, we could either leave it blank or specify 2500.

hope this helps!