GROMACS version: 2023.3
GROMACS modification: No
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We have a molecular system of :
1 ligand (67 atoms) + 1 protein (537 atoms) + appoximately 25000 water molecules (75000 atoms).
Since we interested in molecular dynamic interactions/binding energy and secondary structures, and considering that it depends of many parameters, what would be a typical minimal or approximate average calculation times to get reliable results (in microseconds)? Thanks
There is no such standard time for this. There are pubications from 100 ns to more than microsecond, depends on your protein/receptor and what you are looking for., also your computational fascility.
I would start with atleast 500 ns or 1 microsecond, if i have enough computational or multiple simulations with different initial velocity/position.