AMBER Archive (2009)
Subject: [AMBER] part of the protein escaped from the water box
From: qiaoyan (qiaoyan_at_dicp.ac.cn)
Date: Thu Oct 15 2009 - 06:33:00 CDT
I simulate a protein including 104 residues, the protein was surrounded by a periodic box of water molecules described by the TIP3P potential extended to a distance of 10.0A from any solute atom. After 6ns of constant-pressure simulation, part of the protein escaped from the waterbox, I don't know whether this phenomenon affect the result, please help me,thank you!
The script I use is as follows:
Have a nice day!
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