[gmx-users] Re: change in the secondary structure after simulation

[Mark Abraham]

On 01/27/11, bharat gupta  <bharat.85.monu at gmail.com> wrote:
> Hi,
>  
> I did a 3ns simulation of a 236 amino acid protein (GFP, a beta barrel protein), after checking the trajectory it seems that from the first frame itself almost half portion of the two beta strands (159-171, 174-187) of GFP got converted into a loop like structure .. which should not happen in general.. and this change is found to be present from the first frame itself... 
> 

If it's in the first frame, when was it written and how does it compare to the coordinates you gave to grompp?

Mark


> So I want to know where can the fault be ... I followed the instructions for simulation from the lysozyme tutorial.. Pls help ..
> 
> 
> -- 
> Bharat
> Ph.D. Candidate
> 
> 
> 
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