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

[He, Yang]

Hi all users,

I am dealing with  the CG DNA model and I just list the parameters for non-bond potential blow:

  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.

Thank you for any suggestions in advance.

Yang