Subject: the solvate problem in EGO MD program

From: shen Lingling <[email-masked]>
Date: Thu, 29 Mar 2001 16:19:54 +0800

Hi, I am using program EGO to do protein molecular dynamic simulation. In this program package, it add water molecular to the molecular surface of protein  with a certain thinkness. then the water were cut into spheric or cubic shape to get regular countier condition. After all that, my water sphere happened a density hetero-distribution during the following MD simulation. It even developed a vacuum hole at one side of the protein while water density on the other places are enhanced. Neither the total number of water molecular nor the shape of the water solution are changed. How is this happening and what will be the effects on the simulation? I will appreciate for any suggestion.