[gmx-users] Brownian dynamics]

Michel Fodje michel.fodje at mbfys.lu.se
Wed Feb 13 16:48:48 CET 2002

> 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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