[gmx-users] Help with energy minimizing protein in water box with CA2+
Mark.Abraham at anu.edu.au
Wed Nov 21 09:25:59 CET 2007
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?
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.
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