[gmx-users] bonds braking

[Justin Lemkul]

On 10/15/12 8:09 AM, Eduardo Oliveira wrote:
> Hi,
>
> I'm having trouble simulating a protein kinase on water. During the simulation, the molecule moves towards the box limits and some residues apear on the other side. Almost like they are interacting with water molecules on different sides of the box. I'm on my third simulation and the problem persists. I've already tried changing the periodic conditions but with no success. Waht are your thoughts on that?
>
> For additional information:
> Before the dynamics step I performed 4 minimization steps then i did water dynamics and the entire system dynamics.
> Here is all the ".mdp " files.
>
> Sorry in advance for the long email.
>

This is a perfectly normal consequence of PBC.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================