AMBER Archive (2001)

Subject: iwrap & TIP3P model water

From: Xiaolin Chuang (xiaolin_chuang_at_hotmail.com)
Date: Fri Jun 22 2001 - 11:20:06 CDT

Dear Amber users,

Could anyone let me know that;

1. Normally, in your simulation for DNA system (e.g. 1-2 nanosecond), you
image molecules or not (iwrap=0 or 1)? I don't know if I should image.
Please tell me for advantage and disadvantage.

2. As I know, TIP3P water molecules were treated as rigid molecules. This
mean that waters should move with only translation, not rotation. However,
as I saw an animation of a trajectory, water molecules move by translation
and rotation as well. Could you please tell me that how waters were treated
during simulation?

Any suggestion is appreciated. Thank you very much in advance.

Xiaolin
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