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

[Mark Abraham]

Peggy Yao wrote:
> Dear Gromacs users,
>  
> Thanks for earlier help on this problem.
>  
> I have tried a number of approaches with varying results (all bad, 
> unfortunately).  I am trying to add two CA2+ ions to my protein (1k9p), 
> but when I did this genion put the two CA2+ ions very close together and 
> they flew apart.  Then I tried putting only one CA2+, thinking that it 
> would stay put.  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?  

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

One thing I haven't tried yet is adding a few CL- ions
> to make the box neutral .. somehow I don't feel this is the problem 
> though since I've run non-neutral analyses before without such 
> disastrous consequences.  
>  
> Could anyone give me some advice?  I'm at my wit's end.  I am attaching 
> my script below.  Basically fws_ca.pdb is fine, but fws_b4ion.pdb has 
> CA2+ outside of the water box.  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. 

Regularity is likely still there from the way that genbox takes a small 
chunk of water and tessellates it to make your simulation box. It will 
go away once you generate random velocities when you equilibrate.

Mark