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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
