[gmx-users] A problem with periodic boundary conditions
olehtone at focus.hut.fi
Tue Jun 13 15:31:23 CEST 2006
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.
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