[gmx-users] Brownian dynamics]
David L. Bostick
dbostick at physics.unc.edu
Wed Feb 13 18:34:44 CET 2002
Perhaps there is some bond missing in your topology. Can you dump out a
configuration and look at it graphically? If you see something flying
away, then maybe you can pinpoint the problem.
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
On 13 Feb 2002, Michel Fodje wrote:
> > That is a pretty undeniable indication that there is something
> > seriously wrong with your starting structure: the 'outer' two atoms
> > of a series of four bonded atoms (A1 and A4 in A1-A2-A3-A4) should
> > normally be no further than 3 times your average bondlength apart,
> > say roughly 3*0.15 nm = 0.45 nm, not nearly 1 nm...
> I have done minimization before the dynamics.
> My starting structure is an X-ray structure with 5 ZN2+ ions placed
> randomly within a 1nm thich shell that is at least 1nm from the surface
> of the protein;
> This is the procedure I use:
> - pdb2gmx : gromos vacuumm force field
> - grompp with em.mdp -"-
> - mdrun em
> - mdrun bd
> Running mdrun with -debug option does not give any extra information.
> Thanks for all the help,
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