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:
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.
Then your model physics are unrealistic. Either the parameters are wrong, or
your .mdp options are inappropriate. Do your nucleotides really just consist of
three particles (base, sugar, and phosphate)? If so, you may be missing some of
the subtleties of hydrogen bonding (which is an electrostatic interaction), and
the geometry within the helix, and perhaps even causing excessive repulsion
between the phosphate backbones.
-Justin
Thank you for any suggestions in advance.
Yang
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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