AMBER Archive (2005)

Subject: AMBER: Holes in water

From: Lukasz Bielecki (bielecki_at_rose.man.poznan.pl)
Date: Fri Mar 11 2005 - 08:13:40 CST

Dear Amber experts,

When I perform constant pressure MD of a nucleic acid in a TIP3P solvation
box (PME), I get increasing holes or voids in the solvent part of the
system. What can be the reason for this? The system seems to be well
energy minimized, then smoothly heated to 300K, and at those initial
stages no holes appear, only during the later production run.

Many thanks for your help,

Dr. Lukasz Bielecki
Polish Academy of Sciences, Poznan, Poland
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