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19 Nov 2019
Question 4 To model the collective behaviour of large-scale systems such as the flow of polymers or the phase behaviour of lipids and surfactants in water so-called coarse-grained (CG) models are often used. In these models multiple atoms are combined into a single interaction site. One such CG force field is the MARTINI model. In this model 3 or 4 heavy atoms (C, O, N, S etc.) are combined in to a single site as illustrated in the pictures below. For example, four normal water molecules are represented by 1 CG water. A common lipid is represented by 10 sites. All interactions between the particles are modelled as Lennard-Jones interactions. The particles do not have charges (Total for Question 4 2 marks) Coarse-grained water 4 waters = l site All-atom model 118 atoms Coarse-grained model 10 sites (a) One reason is that longer time steps can be used to integrate Newton's equations of motion. If 4 water molecules are combined into a single CG water site the total mass of the particle will be 4x18 or 72 amu. If a 2 fs time step can be used for liquid water at 300K what time step would be appropriate for CG water based on consideration of the mass alone. Why? (b) Another reason why the MARTINI model enables larger systems and longer time scales to be simulated is that less pairs of interactions must be calculated. Estimate the speed up factor between a simulation of a box of atomic water and the same box of MARTINII COG of water based on the generation of a pairlist. (d) Although coarse-grained models such as MARTINI can be used to simulate large systems over long time scales the range of properties that can be investigated is reduced. List 2 properties of a systems that can be obtained at an atomic level for which for which the MARTINI model would not be appropriate and why
Question 4 To model the collective behaviour of large-scale systems such as the flow of polymers or the phase behaviour of lipids and surfactants in water so-called coarse-grained (CG) models are often used. In these models multiple atoms are combined into a single interaction site. One such CG force field is the MARTINI model. In this model 3 or 4 heavy atoms (C, O, N, S etc.) are combined in to a single site as illustrated in the pictures below. For example, four normal water molecules are represented by 1 CG water. A common lipid is represented by 10 sites. All interactions between the particles are modelled as Lennard-Jones interactions. The particles do not have charges (Total for Question 4 2 marks) Coarse-grained water 4 waters = l site All-atom model 118 atoms Coarse-grained model 10 sites (a) One reason is that longer time steps can be used to integrate Newton's equations of motion. If 4 water molecules are combined into a single CG water site the total mass of the particle will be 4x18 or 72 amu. If a 2 fs time step can be used for liquid water at 300K what time step would be appropriate for CG water based on consideration of the mass alone. Why? (b) Another reason why the MARTINI model enables larger systems and longer time scales to be simulated is that less pairs of interactions must be calculated. Estimate the speed up factor between a simulation of a box of atomic water and the same box of MARTINII COG of water based on the generation of a pairlist. (d) Although coarse-grained models such as MARTINI can be used to simulate large systems over long time scales the range of properties that can be investigated is reduced. List 2 properties of a systems that can be obtained at an atomic level for which for which the MARTINI model would not be appropriate and why