[gmx-users] Cannot minimiza - vdwradii.dat ???

Justin Lemkul jalemkul at vt.edu
Thu Nov 15 16:27:26 CET 2012

On 11/15/12 10:26 AM, Steven Neumann wrote:
> I tried both options and now different atom is responsible of this
> (Oxygen from small molecule next to Fe). With nstxout = 1 I observed
> the trajectory -> My Fe(2+) is coming very close to the Oxygen atom
> and it looks that their coordinate became equal: in VMD Oxygen absorbs
> Fe(2+) and the atom disappears :) Any suggestions?

It sounds like the Fe-O interaction is insufficiently repulsive.  What 
parameters are you using for the Fe?  These ions (and transition metals in 
general) are usually very poorly described by most MD force fields.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list