[gmx-users] dihedral angle restraints

Yujie Wu yujie.wu at hec.utah.edu
Wed Nov 2 19:10:22 CET 2005


I am adding a harmonic dihedral angle restraints into gromacs. This
restraint will "pull" a selected dihedral angle from one value to
another (by changing the equilibrium value of the angle). My simulations
seem very unstable: they always end up with a "nan" error (after a few
or tens of ps), which, I'm pretty sure, is not due to my coding error.
It might be due to the "fast" pulling rate, but it seems already quite
slow (45 deg/ns). So I am wondering if I miss something important. Does
anyone here have any experience about this or similar problems? And any
advice on how to solve it? Thanks in advance.

Best regards,


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