[gmx-users] problem in pdb file after SA

Homa Azizian hazizian at razi.tums.ac.ir
Tue Mar 10 06:17:31 CET 2009

Hi all

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.

Thank you in advance for your help. 

Tehran University of Medical Sciences

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