[gmx-users] sudden jumps in RMSD etc.

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jan 19 23:32:39 CET 2012

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 
which you can adapt to your needs.


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