Dear amber users,
I am trying to calculate the density distribution of all the OP1 and OP2
atoms of the DNA around the Z-axis. To do this i am using cpptraj, in that
i am writing the following commands :-
>parm dna-cu1.prmtop
>trajin prod10newns.nc
>density out op1_op2_density.dat number delta 0.25 ".OP1,OP2"
>go
>quit
In the output file i got the following things:-
(here i am showing some initial output and some last output"s data)
Z .OP1,OP2 sd(.OP1,OP2)
-0.0050 0.0000 0.0000
0.0050 0.0000 0.0000
0.0150 0.0000 0.0000
0.0250 0.0000 0.0000
0.0350 0.0000 0.0000
0.0450 0.0000 0.0000
0.0550 0.0000 0.0000
0.0650 0.0000 0.0000
0.0750 0.0000 0.0000
. . .
. . .
. . .
74.5850 0.0000 0.0000
74.5950 0.0000 0.0000
74.6050 0.0000 0.0000
74.6150 0.0000 0.0000
74.6250 0.0000 0.0000
74.6350 0.0000 0.0000
74.6450 0.0200 0.0141
74.6550 0.0000 0.0000
I am not able to understand what I am getting in the first column, but the
box's z axis length is 104.
*-------------------------------------------------*
*With Regards*
*Angad Sharma*
*Research Scholar*
*School of Computational & Integrative Sciences*
*Jawaharlal Nehru University*
*New Delhi 110067, (INDIA)*
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Received on Mon Feb 06 2023 - 10:00:02 PST
