Date: Mon, 13 Apr 2009 12:37:21 +0100
Dear Amber !
I am doing targeted molecular dynamics
in explicit water
I have two structures from the same
sequence of DNA ,
I have added TIP3P water to both the
structures in truncated octahedron geometry . Minimized and
equilibrated.,
The number of molecules in both of them
are equal , when the targeted molecular dynamics is
given with periodic boundary condition
, the water molecules are not bound together with the DNA, I have
attached the picture with this ,
I have seen the DNA tutorial , its
possible to re image the trajectory with ptraj .
I have attached my input file , if i am
doing some mistakes in flag
let me know
thanks in advance
regards
balaji
UOM
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(image/png attachment: Screenshot.png)
- text/plain attachment: ATT00002.txt
