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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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