AMBER Archive (2005)

Subject: Re :AMBER: Holes in water

From: Pascal Auffinger (P.Auffinger_at_ibmc.u-strasbg.fr)
Date: Fri Mar 11 2005 - 09:26:31 CST

Well its quite easy. During the setting up of the system there is just no
way to get an optimal compaction of the solvent. Then during the MD the
system compacts itself, especially around the solute and then you get see
the formation of holes since the box size (pressure) cannot adjust.

Pascal

> 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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________________________
pascal auffinger
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