In NAMD- linear interaction energy, we perform two sets of simulations- protein+ligand complex in water and free ligand in water. If I have performed my simulation of the complex for 100ns, is it mandatory that the free-ligand simulations must also be performed for the same 100ns?
Kindly provide your valuable suggestions.
Thanks in advance.
In my openion, you should have to perform the ligand simulation for the same time as you have done with prot-lig complex and introduce as few differences between both simulations as possible.
If you want to perform long bound simulations (e.g. 100 ns), I would argue that unbound simulations do not necessarily need same simulation lengths as for the bound ones. The idea of performing MD for LIE is to extract energetic terms i.e. van der waals and electrostatic energies, and bound simulations may need longer simulation time to reach convergence since they have more complex condition (interacting with protein) compared to unbound simulations (free in water)
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