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
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