[gmx-users] RMSD graph

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jun 18 06:10:03 CEST 2008

Anamika Awasthi wrote:
> Dear All,
>        Please tell, what should I predict from this graph?

We can't tell from your graph what's happening because you haven't told 
us how you generated it. It's also not our job to do so - it's yours. 
You can go at look at your data at the points that have "interesting" 
behaviour and see what is causing that. We can't.

>        I can understand this is normal type of graph.
>        Sorry for inconvenience, but I want to ask some questions,
> my this job crashed many time, because of power shut down and I had to 
> restart this again and again, I used tpbconv for the same.

> but now when I was trying to get rmsd plot from my running job..its not 
> reading the tpr file, which I got from tpbconv , its reading previous 
> tpr file.

It's doing what you're telling it to do. No more, no less.

If you don't tell us exactly what you were doing and what you were 
trying to do, we can't offer any insight into the failure.

> Is it okey?

No. I guess wildly that you need to correct for periodicity effects, see 


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