Molecular Modeling and Bioinformatics Group

Nucleic Acid Data:

Sequence	CGCGAATTCGCG
Rev. Sequence	CGCGAATTCGCG
Type	DNA
SubType	B
Chains	duplex
Pdb	1NAJ [PDB] [NDB]
Ligands	No
Keywords	DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral

MD Simulation >> (Click to expand/shrink)

Simulation Metadata
Force Field	parmBSC1
Simulation Date	2015-May-07
Simulated Time	800 ns
Time Step	1 ps
Parts	DNA+ions
Temperature	298K
Water	TIP3P
Additional Solvent	No
Counter Ions	Na+
Ionic Concentration	Electroneutrality
Additional Ions	No
Additional Molecules	No
Ions Parameters	Dang

Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)

Simulation Metadata (UMM)
AdditionalIons	No
AdditionalMolecules	No
AdditionalSolvent	No
Author	I.I.
Chains	duplex
Comments	-
CounterIons	Na+
Format	mdcrd
FrameStep	1 ps
Frames	800000
IonicConcentration	Electroneutrality
IonsParameters	Dang
Ligands	No
NucType	DNA
PDB	1NAJ
Parts	DNA+ions
RMSd_avg	1.787
RMSd_stdev	0.353
Rgyr_avg	13.380
Rgyr_stdev	0.261
SASA_avg	4383.518
SASA_stdev	69.231
SubType	B
Temperature	298K
Topology	DDD_800ns_replica.prmtop
Trajectory	DDD_800ns_replica.mdcrd
Water	TIP3P
_id	NAFlex_DDD_800ns
altPDB	101D 109D 127D 128D 129D 130D 144D 166D 170D 171D 1BNA 1D30 1D43 1D44 1D45 1D46 1D64 1D85 1D86 1DAU 1DNH 1DOU 1DPN 1DUF 1EDR 1EEL 1EHV 1EI4 1FMQ 1FMS 1FQ2 1FTD 1G3X 1GIP 1I3T 1I47 1JGR 1LEX 1LEY 1M6F 1N1O 1NAJ 1NGT 1PRP 1QV4 1QV8 1QXB 1VE8 1VZK 1ZPH 1ZPI 227D 233D 265D 266D 267D 268D 269D 270D 289D 290D 291D 298D 2B0K 2B3E 2BNA 2DAU 2DBE 2DYW 2GVR 2GYX 2I2I 2I5A 2L7D 2NLM 2QEG 2RF3 2RMQ 302D 303D 311D 328D 355D 360D 388D 389D 3BNA 3D0P 3OIE 3OPI 3U05 3U08 3U0U 3U2N 426D 428D 436D 442D 443D 444D 445D 447D 448D 449D 453D 455D 457D 460D 461D 463D 478D 4AGZ 4BNA 4C63 4C64 4DNB 4GJU 4GLG 4MKW 4OPJ 4QC7 4U8A 4U8B 4U8C 5BNA 6BNA 7BNA 8BNA 9BNA
authors	Ivan Ivani, Pablo D. Dans, Agnès Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluís Gelpí, Carlos González, Michele Vendruscolo, Charles A. Laughton, Sarah A. Harris, David A. Case and Modesto Orozco
dataset	Array
date	2015-May-07
description	DNA-B Duplex Naked DDD ParmBSC1 TIP3P Electroneutral
forceField	parmBSC1
ionsModel	-
moleculeType	Dna
rev_sequence	CGCGAATTCGCG
saltConcentration	-
sequence	CGCGAATTCGCG
soluteAtoms	758
soluteCharge	-22
soluteResidues	24
solventAtoms	-
solventResidues	-
time	800
totalAtoms	758
totalCharge	-22
totalIons	-
totalResidues	24