[Bulk] [gmx-users] RMSD graph

Yang Ye leafyoung at yahoo.com
Wed Jun 18 07:55:37 CEST 2008

Quite likely, it is due to part of molecule moving "out of box". Also, 
the molecule could be of multiple chain.

So you need to find a way to put the whole molecule in one piece. Try 
various options from trjconv -pbc. If it is DNA, a trick is to define 
one chain as an index group and then center that group.

Yang Ye

Anamika Awasthi wrote:
> Dear All,
>        Please tell, what should I predict from this graph?
>        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.
> Is it okey?
>   Thanks in advance
>          Anamika
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