Thanks for reply
>
>> 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
If I use this command and viualize processed trajectory in VMD will it tell me
the water molcule which
I have selected by closest command are actualy present closest to mask atom.
Since in every frame water molecules are changing.
Here my aim is to identify water molecule near to mask atom and do MMPBSA on
considring these water molecules.
So I am confused here either to use above command or use VMD to identify that
water molecule since water moleclue
cahnging in each frame.
>
>> 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...
>
Yes you are right I have used the wrong approach. Actualy I have selected water
molecule at zero frame in VMD for visualizing it upto last frame later I
realized that water molcule were changing
in each frame.
>
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With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Wed May 18 2011 - 23:30:02 PDT
