Hello all
I have cofusion about ptraj command.
I have used command:
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
2)
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
When I visualized both processed trajecory in vmd using command all within 5 of
rsid 78, 8, 9
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
Since I have used the same command except closest and water moleclues which are
existing between them are within 5 angostrom
then why I am not able to see water molecule existance for 1-2000ps for command 1)?
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 15 2011 - 05:30:02 PDT
