Effect of warmup protocol and sampling time on convergence of molecular dynamics simulations of a DNA dodecamer using AMBER 4.1 and particle-mesh Ewald method.
J Biomol Struct Dyn
; 14(5): 607-11, 1997 Apr.
Article
en En
| MEDLINE
| ID: mdl-9130082
ABSTRACT
This report describes one 3000 ps and two 1500 ps molecular dynamic simulations on a TATA box containing dodecamer DNA duplex in a periodic box of TIP3P water molecules, using the AMBER 4.1 implementation of the particle-mesh Ewald method. We compare the effect of warmup protocol and simulation time length on the root-mean square deviation (RMSD) parameter. For the longer simulation, the RMSD computed for the 500-1000 ps time interval is representative of longer time intervals, including 500-3000 ps. The various warmup protocols do not appear to have a significant effect on the simulation results. Based on the present results, DNA sequence-dependent differences in RMSD, or related properties, should exceed two standard deviations before being attributed to non-simulation factors, such as warmup protocol and sampling time effects; we recommend a minimum criterion of at least a three standard deviation difference with a sampling period of at least 500-1000 ps. In addition, while end effects appear negligible there is a consistent dependence of RMSD on DNA helix length.
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Banco de datos:
MEDLINE
Asunto principal:
Oligodesoxirribonucleótidos
/
ADN
/
TATA Box
/
Conformación de Ácido Nucleico
Tipo de estudio:
Prognostic_studies
Idioma:
En
Año:
1997
Tipo del documento:
Article