Dear Chris,
I did not post the redmine issue yet, I want to check every possibility
beforehand. I will analyze trajectories more closely now.
Best,
Grzegorz
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?
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
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