> 1)
> trajin NPT-1.mdcrd 1 2000 1
> center :78.HE21 mass origin
> center :8.O4 mass origin
> center :9.O6 mass origin
>
> image origin center familiar
> trajout NPT-1_center.mdcrd mdcrd
Only that last center command is relevant since each time center is called
it moves the coordinates of the selected group of atoms to the center.
Essentially you are moving the coordinates three times, and at the end
:9.O6 is the center.
> center :78.NE2 mass origin
> center :8.O4 mass origin
> center :9.O6 mass origin
>
> image origin center familiar
> strip :Na+
> closest 10 :78.NE2 first noimage
> closest 10 :8.O4 first noimage
> closest 10 :9.O6 first noimage
> trajout NPT-1-close-78.NE2-8.O4-9.O6.mdcrd mdcrd
Here again we run a command three times, however once you've already run
the first, you only have 10 waters left so that is the only one that
matters... You likely want to run
center :78.NE2,:8.O4,:9.O6 mass origin
image origin center familiar
closest 10 :78.NE2,:8.O4,:9.O6 first noimage
> in case of command 1)one water molecule was existing between thwm for 1-1000ps but
> in case of command 2)water molecule wtith exchanging their position bwteen them
> are existing for 1 - 2000ps
How are you determining the lifetime? Note that the closest command does
not retain the water identity so although a water may be in a similar
place, it is not necessarily the "same" water, i.e. you cannot look at
lifetimes...
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Received on Wed May 18 2011 - 14:00:02 PDT
