I am studying the effect of organic co-solvents on the activity of enzymes, I want to perform short MD simulation. Is it possible to simulate large proteins in water or organic solvents using NAMD? If yes what are the minimum computational requirements to do this?
thanks
Dear Ghada,
Yes, it is possible to simulate your protein in water and organic solvent. In water is quite simple to set up the system, but unfortunatelly I am not sure about how difficult is set up your system in organic solvent. You should check if the desired force field provides you parametrized organic solvents and how to set up.
Basically you can start running your MD simulations in computers like Core I7 or Xeon. I used these machines and normaly it takes longer times to run. If you have access to one cluster it will be faster to do this job. For example one system with about 40.000 atoms using one Core i7 I can run 1ns per day. In one big cluster using 512 cores I can run 10 ns per day.
I think these papers could help you:
Soares, C.M., Teixeira, V.H., Baptista, A.M. (2003) "Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies", Biophys. J., 84, 1628-1641
Lousa, D., Baptista, A.M., Soares, C.M. (2011) “Structural determinants of ligand imprinting: A molecular dynamics simulation study of subtilisin in aqueous and apolar solvents”, Prot. Sci., 20, 379-386
Yes you can perform MD simulation of the protein in the desired solvent system. The system requirements to perform MD simulation of a protein of your length in NAMD for 10ns should be minimum 4GB RAM dual core, or you can try BioLinux there its much faster.
@Danilo Olivier
40.000 atoms at one processor - 1ns per day? It sounds fantastic. Maybe you mean some extreme cutoff?
Dear Alexey,
I am sorry, but I think was not clear enough. I meant using all cores of one Core I7 I reached 1ns per day in one system with about 40.000 atoms. Does it sound more realistic?
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