[gmx-users] sudden jumps in RMSD etc.

[Mark Abraham]

On 20/01/2012 7:55 AM, Yun Shi wrote:
> Hi all,
>
> I am doing duplicate MD simulations with a protein-ligand system.
>
> After processing one trajectory by trjconv with the optioin -pbc 
> nojump, I still find abrupt jumps (on the scale of nm) in RMSDs and 
> COM distances.
>
> Then I tried -pbc mol -ur compact, which did not work. And then -fit 
> progressive on protein atoms, which again did not completely eliminate 
> those jumps in protein atom RMSDs.
>
> I wonder if I have not used the right option?

There's a suggested workflow here 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions 
which you can adapt to your needs.

Mark