[gmx-users] problem in pdb file after SA

Diego Enry Gomes diego.enry at gmail.com
Tue Mar 10 09:44:32 CET 2009

You mean that half the protein is in one side of your cubic box and  
the other half is on the other side ?
Try removing PBC or fitting to a reference frame (like the one before  
SA). Search the list archives, this is a very common question.

On Mar 9, 2009, at 10:17 PM, Homa Azizian wrote:

> I have done MD job on a 226 residue protein with cubic box -d 0.9 in  
> the
> editconf step.
> after 30 ns I entered the last step pdb to the simulating annealing,  
> again
> with cubic box and -d 0.9. the highest temp was 600 K and the loest  
> was 50 K.
> When I see the pdb of structures at 300 K, 600 K and 50 K in pymol,  
> it seems
> the structures converts to 2 part, one along oneside of cubic's  
> surface the
> other was in the parallel side, I mean that the system move out of  
> the cubic,
> and the outer part appears in another side of cubic, so I dont have  
> the
> integrate structure.
> How can I fix this problem.

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