[gmx-users] OPLS/AA + TIP5P, anybody?
gigo at ibb.waw.pl
Sun Sep 29 22:27:28 CEST 2013
I did not post the redmine issue yet, I want to check every possibility
beforehand. I will analyze trajectories more closely now.
On 2013-09-29 18:47, Christopher Neale wrote:
> 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?
> -- 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,
> 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
> 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,
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