[gmx-users] peptide goes out of box after md simulation
Mark.Abraham at anu.edu.au
Mon Nov 24 05:45:42 CET 2008
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.
> 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
I don't know what you mean.
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