[gmx-users] Help with energy minimizing protein in water box with CA2+
tsjerkw at gmail.com
Wed Nov 21 09:18:40 CET 2007
You really have to do some background reading on molecular dynamics
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?
> 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
> 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
> Many thanks for any help..
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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