Hi, I have rather elementary questions regarding force constants used in restraining position/orientation:
- I have imposed a force with constants kx, ky, and kz =10^6 kJ/mol/nm^2 on a particular atom of a peptide to harmonically position restrain the molecule inside a bilayer. Is it alright to use such high values for force constants? I have used kz =10^3 kJ/mol/nm^2 but it seems that the peptide can still move 2-3 angstrom up and down during the course of 200ps simulation so I needed to restrain it more tightly. - If I calculate PMF along the z-coordinate (performing separate MD's for the peptide along z axis) -- assuming i get reasonable overlaps for the histograms -- would such a large number create (numerical) problems in WHAM calculations? - what is a typical force constant to use in angle_restraint_z (referring to formula 4.68 in 3.3 manual). Considering the units of k_c, is 500kJ/mol way off? -- Cheers, Terry
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