[gmx-users] Help with energy minimizing protein in water box with CA2+

[Tsjerk Wassenaar]

Peggy,

You really have to do some background reading on molecular dynamics
simulations...

 After I ran an energy minimization, the CA2+ ended up outside of the box.
> Now I am really perplexed.  What could be causing this behavior?
>

See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions


> Could anyone give me some advice?  I'm at my wit's end.
>

Start with normal MD simulations, without bothering about calcium.
Later on, take your protein and put the calcium in by hand in the place(s)
it should be. You can infer the coordinates from those of the coordinating
oxygens.


> The water in the water box looks like ice cubes in an ice cube tray,
> segregated into regular little mini-boxes.  I presume the latter is a
> numerical consequence of the CA2+ flying out of the box.
>

Very wrong. It's a consequence of building up a water box from smaller water
boxes.


>
> Many thanks for any help..
>
> Peggy
>
>

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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