[gmx-users] dihedral angle restraints
spoel at xray.bmc.uu.se
Fri Nov 4 08:35:00 CET 2005
On Wed, 2005-11-02 at 11:10 -0700, Yujie Wu wrote:
> 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.
How is this different from what is in gmx 3.3?
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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