Bhawana Gupta wrote:
hello everyone,
After doing md simulation with no. of steps 1 ns ,my peptide which is of
7-8 residue move out of the boundary of water box.
tell me what shd i do get rid of this problem.
See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
Also i want to know about the wall of the box, whether it is permeable
or semi-permiable.
this is very silly question.
Yup. It's a mathematical construct.
Is there something, from which i can know about the dimension of the box
and about the membrane so that i can change it when i have to simulate a
peptide
I don't know what you mean.
Mark
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