[gmx-users] peptide is going outside of box

Mark Abraham mark.abraham at anu.edu.au
Wed Feb 27 13:54:46 CET 2008

> Hi all,
>  I have to simulate peptide with SPC water model.During the simulation
> trajectory peptide is some time going out of box through periodic
> boundary condition is there but physical prescence of solvent is not
> there, i mean if i have to extract water molecule within 3 angstrong
> cutoff of peptide then it is not possible in all trajectory because of
> some steps in which peptide is outside of box.I want to fix one of atom
> in a box so that all in a process of folding simulation peptide will
> remain inside of box.
>    I will be thankful for any positive response.

See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions


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