Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure

Journal of Physical Chemistry B

Volumn 110, Issue 23, 2006, Pages 11571-11581

  Babin, Volodymyr ^a   Baucom, Jason ^a   Darden, Thomas A ^b   Sagui, Celeste ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; COMPUTER SIMULATION; CRYSTALLOGRAPHY; ELECTRIC FIELD EFFECTS; ELECTROSTATICS; MOLECULAR DYNAMICS;

CRYSTALLOGRAPHIC STRUCTURE; MOLECULAR DYNAMICS SIMULATIONS; POLARIZABLE FORCE FIELDS; ROOT-MEAN-SQUARED COORDINATES DEVIATIONS (RMSD);

DNA;

EID: 33745727284     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp061421r     Document Type: Article

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53. [The standard deviations (SD) are computed as the second moments of the distribution. To obtain an estimate of error of measurement of the mean value, one would have to compute the SD from a group of independent sampling points and then divide by the square root of the number of sampling events. For instance, if the configurations stored every 1 ps were independent, the error of the mean value during the last 10 ns of the simulations could be obtained by dividing the reported SD by √10 000 = 100. Of course, these configurations are not independent and one has to carry block averages, and the SD tend to increase with the size of the block. We find that for block sizes as large as 3.5 ns, the error estimate is approximately only 5 times worse than the one computed in 1 -ps windows. Even if one assumes that the real error is 10 times worse than that for the 1-ps windows, one would still have to divide the SD in Table 2 by approximately 10, which gives very small values for the error of measurement of the mean value.
54. In the mixed systems, mix-99 and mix-02, the duplexes strongly interact in a complex way (whose study is beyond the scope of the present work) and are not analyzed here.
55. Even in the ideal structure of B-DNA, the base pairs are not geometrically identical in terms of bond lengths, valence angles, complementary parameters. For example, the coordinate frame of a standard guanine is slightly different from a standard adenine and the base pairs are not coplanar nor perfectly aligned perpendicular to the double helical axis. The twist of consecutive base-pair frames can thus be slightly sensitive to sequence, due to the definition of the standard base (and base-pair) frame. If, instead of using a local helical axis at each base-pair step, a global linear helical axis is used, ABDNA produces the ideal value of 36°.