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Studying protein-polymer assembly using Dry Martin
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7 years 7 months ago #5874
by debaduttaprusty
Studying protein-polymer assembly using Dry Martin was created by debaduttaprusty
Hi,
I am trying to study the aggregation behaviour of proteins in the presence of polymers. Since I am using a protein:polymer ratio of 1:20 (as used by experimental collaborators), using an implicit Martini model will allow me to simulate large systems. In my case, each protein has 1394 Martini beads and each polymer around 250. The dry martini parameters that are available slightly differ from the original Martini with two more interactions levels being present in the former.If I use wet Martini, for 10 proteins and 200 polymer chains, I will be using around 1.2 million water beads. I was wondering whether it is possible to use Dry Martini values for simulating the above system since it takes away the burden of computing interactions involving solvent beads. As for the coarse graining of my polymer, I can generate coarse-grained parameters for implicit solvent by matching its partition coefficient and the one generated from all atom model and a few structural properties (such as radius of gyration and bond angle distribution, etc.). Does it sound reasonable?
Thanks,
Debadutta Prusty
I am trying to study the aggregation behaviour of proteins in the presence of polymers. Since I am using a protein:polymer ratio of 1:20 (as used by experimental collaborators), using an implicit Martini model will allow me to simulate large systems. In my case, each protein has 1394 Martini beads and each polymer around 250. The dry martini parameters that are available slightly differ from the original Martini with two more interactions levels being present in the former.If I use wet Martini, for 10 proteins and 200 polymer chains, I will be using around 1.2 million water beads. I was wondering whether it is possible to use Dry Martini values for simulating the above system since it takes away the burden of computing interactions involving solvent beads. As for the coarse graining of my polymer, I can generate coarse-grained parameters for implicit solvent by matching its partition coefficient and the one generated from all atom model and a few structural properties (such as radius of gyration and bond angle distribution, etc.). Does it sound reasonable?
Thanks,
Debadutta Prusty
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