I have performed simulations for Protein RNA complex around 1500 residues. I have used triclinic box with 1.4 nm distance from the edge of the box to protein as triclinic box takes less number of water molecules compared to other boxes ~100000. The simulation results looks fine and i am able to answer the biological question. however i have not seen many publications using triclinic box. Hence i am bit skeptical and like to know there is any criteria to choose the simulation box.
Thanks
There really is no criteria as such. The idea is to perform the simulation in the most efficient way possible. If you do not have access to the computational power required for higher order boxes and the triclinic is answering the question which you posed, you are fine.
But yes, if you can computationally simulate the upper tiers then all for the better.
Just make sure that you account for the minimum image convention since you will be using periodic boundary conditions. That is all that matters.
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