AMBER Archive (2001)

Subject: DNA Simulation

From: Troy Bothwell (tbothwe1_at_bigred.unl.edu)
Date: Mon Jan 08 2001 - 15:20:16 CST

During a 2ns simulation of a 14-mer dna duplx, part of the solute "floated"
outside the periodic box of water. The strands remained together. Does
anyone know what causes this? The boundaries are 10 angstroms away from the
duplex on all sides initially.

Thanks for any input,

Troy Bothwell
Graduate Student
University of Nebraska Lincoln