[gmx-users] peptide goes out of box after md simulation

Mark Abraham 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.

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.


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