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
go
trajin md.mdcrd
trajout test1.mdcrd
center 1-25
image familiar
go
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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Received on Sun Dec 03 2006 - 06:07:38 PST
