From: Atsutoshi Okabe <okabe.cherry.bio.titech.ac.jp>
Date: Sat, 14 Oct 2006 16:31:01 +0900
Dear all,
I want to visualize solvent distributions (i.e distributions of the first
water shell) around one solute molecule.
So I executed the following grid command within ptraj
trajin md.crd
center :1
image
rms first mass out rms :1
grid wat.xplor 100 0.5 100 0.5 100 0.5 :WAT
Then I got the wat.xplor file and visualized the file with chimera soft
ware. (attached files)
But I doubt that I could get the figure I would intend.
Actually I can't understand grid command and the ouput file( wat.xplor file
)
I don't know how I should deside the value of grid point and grid space.
Could you give me any help?
Tnanks
Atsutoshi
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Received on Sun Oct 15 2006 - 06:07:15 PDT
