AMBER Archive (2006)

Subject: AMBER: watershell and image commands

From: Esther Brugger (
Date: Thu Nov 30 2006 - 16:37:58 CST

Hi, everybody,
 I am trying to use "watershell" to calculate the waters in the solvation shells. But one thing is confused me. When I use the "image" command to generate the waters to the primary box, I found 2 different results. One is the molecules in the center of the box, one is not. I am just wondering whether it will influence the "watershell" to calculate the waters. Here are the 2 ways to re-image the trajectory file:
 trajin md.mdcrd.gz
 trajout test2.mdcrd
 center origin :1-25
 image origin familiar
 trajin md.mdcrd
 trajout test1.mdcrd
 center 1-25
 image familiar
 Is there someone know that? Which one will be correct to choose to calculate the "watershell"?
 Thank you very much!

Esther B.

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