[gmx-users] GMX 4.0 RC2: mdrun writes broken molecules?

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 5 16:32:36 CEST 2008


I've been running some simulations with Gromacs 4.0 RC2, and I've noticed 
something strange.  In the output .gro file at the end of a run, the molecules 
in my system (a membrane protein) are broken, crossing periodic boundaries. 
This affects the lipids at the periphery of the box, in my case.

Has there been some change since the previous version that mdrun is now writing 
broken molecules to fit everything within the unit cell?  Or is this behavior 



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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