[gmx-users] Re: change in the secondary structure after simulation
mark.abraham at anu.edu.au
Thu Jan 27 07:49:50 CET 2011
On 01/27/11, bharat gupta <bharat.85.monu at gmail.com> wrote:
> 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?
> So I want to know where can the fault be ... I followed the instructions for simulation from the lysozyme tutorial.. Pls help ..
> Ph.D. Candidate
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