[gmx-users] OPLS/AA + TIP5P, anybody?

[Christopher Neale]

Dear Grzegorz:

Under no conditions should any of the tip5p geometry change (for the standard tip5p model). 
If you find that this is happening, then that is certainly an error. You can check if you like by analyzing 
your trajectory. However, flexible bonds will allow the distance from the arginine N to the arginine
H to vary, which my allow a closer approach of the arginine H to the tip5p dummy site.

Did you verify that a water box (no protein) simulates without error?

Did you post a redmine issue with .mdp , .gro , and .top files?

Chris.

-- original message --

Dear Chris,
Authors answered me very quickly. They did not have such a problem, but 
I still don't know the details of their input. They used gromacs-3.3, so 
I decided to give the old one a try. I did some tests with 3.3.4. 
Although the same problem occurred during steep minimization, some 
interesting things popped out. When I tried to grompp the system with 
plain tip5p for cg minimization, it failed:
"ERROR: can not do Conjugate Gradients with constraints (8484)", even 
though I did not set any constraints. The error is the same for tip4p 
unless you use flexible model, which tip5p does not have - the water had 
to be constrained then. I guess that treatment of virtual sites in 
gromacs-3.3 has something to do with this. I noticed, that constraints 
make simulations with tip5p more stable. It should not happen, that the 
LP virtual atoms are pulled further then the defined 0.7 from the 
oxygen, right? I will keep you updated.
Best Regards,
Grzegorz