Dear Gromacs Users! I want to simulate folding of small globular protein in water.
I have linear structure ( with all psi\ phi torsions set to 180 ) of my peptide made in HyperChem as well as NMR structure ( for control ). Could you tell me what specificities of such simmulation should I take into account ? Could I use parametets from Lyzocyme tutorial for NPT NVT and MD simulation? What average length of the run trajectory should be if my peptide 1) is the simple coil? 2) Has secondary structure- e.g consist of 2 short helicees and one b-sheet Thanks, James
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