[gmx-users] problem in pdb file after SA
hazizian at razi.tums.ac.ir
Tue Mar 10 06:17:31 CET 2009
I have done MD job on a 226 residue protein with cubic box -d 0.9 in the
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
How can I fix this problem.
Thank you in advance for your help.
Tehran University of Medical Sciences
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