periodic boundary conditions with lipids

From: Jee Eun Rim (
Date: Wed Dec 17 2003 - 12:29:45 CST

Hello all,

In simulating lipid systems, does namd have problems with lipid molecules being split across the boundary?

For example, I get bad global exclusion count errors when my system has an initial pdb file with molecules that are wrapped around the boundary, i.e., if parts of a molecule is on one side of the periodic cell, but the rest of the molecule is wrapped around the boundary and appears on the opposite side of the cell.

By the way, I'm using version 2.53.

Thanks for the help,

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