Molecular Modeling and Bioinformatics Group

Nucleic Acid Data:

Sequence	CGCGCGCGCG
Rev. Sequence	CGCGCGCGCG
Type	DNA
SubType	Z
Chains	duplex
Pdb	1I0T [PDB] [NDB]
Ligands	No
Keywords	DNA-Z Duplex Naked ParmBSC1 TIP3P AddedSalt

MD Simulation >> (Click to expand/shrink)

Simulation Metadata
Force Field	parmBSC1
Simulation Date	2015-Apr-25
Simulated Time	946 ns
Time Step	1ps
Parts	DNA
Temperature	300K
Water	TIP3P
Additional Solvent	No
Counter Ions	Na+Cl-
Ionic Concentration	4M
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+Cl-
Format	mdcrd
FrameStep	1ps
Frames	946999
IonicConcentration	4M
IonsParameters	Dang
Ligands	No
NucType	DNA
PDB	1I0T
Parts	DNA
RMSd_avg	3.149
RMSd_stdev	0.995
Rgyr_avg	11.664
Rgyr_stdev	0.650
SASA_avg	3570.048
SASA_stdev	120.702
SubType	Z
Temperature	300K
Topology	no_wat.top
Trajectory	zdna4M/naked.trj.gz
Water	TIP3P
_id	NAFlex_Z-DNA-4M
altPDB	131D 133D 1D24 1D33 1D39 1D48 1DA2 1DCG 1DJ6 1DN4 1DN5 1G3A 1I0T 1I7J 1ICK 1PBL 1PBM 1QDA 1T4X 1TNE 1UQG 1V9G 1VRO 1VTU 1VTV 1WOE 223D 242D 277D 292D 293D 2DCG 2ELG 2IE1 310D 336D 390D 391D 392D 3P4J 3WBO 427D 4FS5 4FS6 4HIF 4HIG 4R15
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-Apr-25
description	DNA-Z Duplex Naked ParmBSC1 TIP3P AddedSalt
forceField	parmBSC1
ionsModel	-
moleculeType	Dna
rev_sequence	CGCGCGCGCG
saltConcentration	-
sequence	CGCGCGCGCG
soluteAtoms	628
soluteCharge	-18
soluteResidues	20
solventAtoms	-
solventResidues	-
time	946
totalAtoms	628
totalCharge	-18
totalIons	-
totalResidues	20