[gmx-users] about the repelling of DNA base pair

[Mark Abraham]

He, Yang wrote:
> Hi all users,
> 
> I am dealing with  the CG DNA model and I just list the parameters for non-bond potential blow:

People may care *which* CG model you are using...

>   A     T         1        0.0069        0.000004109
> 
>   P     P         1        0.000004352   4.352E-12
> 
>   S     S         1        0.000004352   4.352E-12
> 
>   A     A         1        0.000002177   1.0894852E-12
> 
>   T     T         1        0.000002177   1.0894852E-12
>   C     G         1        0.0097        0.000005422
>   C     C         1        0.000002177   1.0894852E-12
>   G     G         1        0.000002177   1.0894852E-12
> 
>   A     S         1        0.000004352   4.352E-12
> 
>   A     P         1        0.000004352   4.352E-12
>   A     C         1        0.000002177   1.0894852E-12
>   A     G         1        0.000002177   1.0894852E-12
> 
>   T     S         1        0.000004352   4.352E-12
> 
>   T     P         1        0.000004352   4.352E-12
>   T     C         1        0.000002177   1.0894852E-12
>   T     G         1        0.000002177   1.0894852E-12
>   C     S         1        0.000004352   4.352E-12
>   C     P         1        0.000004352   4.352E-12
>   G     S         1        0.000004352   4.352E-12
>   G     P         1        0.000004352   4.352E-12
> 
>   S     P         1        0.000004352   4.352E-12
> 
> You can see that the base pair potential is larger than the other pairs . But I found when I run this case,using the command "ngmx",  it always shows that the matching base pair will repel from each other even I set the temperature by 0K in the mdp.file . I have checked the base pairs' distance and originally they are all in the equilibrium distance.

The vdW interactions are only a small part of the story. The 
electrostatics treatment and your equilibration regime are also very 
important.

Mark