Hi
I have been running MD simulations of antimicrobial peptides in both water and in lipid bilayers.
I have noticed that for my MD simulations in water that the calculations are much slower (obtaining trajectories), compared to that of peptides in lipid membranes.
I guess it has to do with the fact that the water molecules move around quicky with little restrictions, compared to the atoms of the lipid molecules. Is that the case? In literature, I found that there are reports that state that proteins in water require less computational resources. So I´m confused.
Any comments? Observations? Or recommended articles?
It can be related to higher degree of freedom (transnational, rotational motions), and PME calculations associated with the water molecules.
Can I ask a follow up? Do you mean that (all-atom?) simulations of a bilayer+peptides+solvent are faster than just solvent+peptides, with all else being identical (number of atoms, timestep, PME, other nonbond parameters like update interval, write frequency, etc)?
Its possible that in simulations of slowly-diffusing lipids, you could be getting away with updating the neighbor list less frequently.
Thanks for the input Erick.
Yes, I am referring to all-atom simulations, comparing solvent+ peptide to sovent+peptide+bilayer. The total number of particles are not identical, but similar. However, the number of water molecules in the solvent-peptide system is much greater that that of the solvent-peptide-bilayer system.
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