[gmx-users] A problem with periodic boundary conditions

Olli Lehtonen olehtone at focus.hut.fi
Tue Jun 13 15:31:23 CEST 2006

Hi all,

While running an energy minimization with mdrun 3.3.1, I observed that
different peptide units in the simulation box were translated in y
direction out of the box, each by N*Ly, N=1,5 (N is peptide unit and Ly is
the box y-dimension). The final structure (confout.gro) is a kind of
staircase instead of beta sheet which I'm trying to simulate.

Only one peptide and all solvent (water and Cl-) remain in the original
box. This happens even after setting nsteps=1. My system is probably quite
far from equilibrium but this kind of behaviour seems anyway unexpected.

I used genconf to generate the initial structure (which looks fine) and it
is these generated units which become translated with mdrun. Any
suggestions how to solve this problem are welcome.

best regards,


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