[gmx-users] range of magnitude for force constant

Terry Nelson terry.b.nelson at gmail.com
Wed Jan 28 12:47:59 CET 2009


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
   - 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?

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