AMBER Archive (2009)

Subject: [AMBER] problem with explicit solvent in TMD

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Mon Apr 13 2009 - 06:37:21 CDT

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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