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
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