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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