# data[].attributes.annote
Probe MD simulations. Mapping an allosteric site at the intracellular side of the Beta2 adrenergic receptor. Beta2 adrenergic receptor in the presence of 10% of butyramide (BTA) in the water-POPC bilayer. 0.15M of Na+ and Cl-. Three replicates are provided. 
Trajectory originally donated to SlimMD

# data[].attributes.title
Beta2 adrenergic receptor in the presence of 10% of butyramide (BTA) 40 ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
DNA minicircle (339 base pairs) with 33 turns 30ns, 100mM CaCl2.
Trajectory originally donated to SlimMD

# data[].attributes.title
DNA minicircle (339 base pairs) with 33 turns 30ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes._psdi_force_fields
AMBER99 for DNA, parmBSC0, parmOL4, parmOL1 corrections for backbone dihedrals, TIP3P water.

# data[].attributes.annote
DNA Minicircle (339 base pairs) with 30 turns 30ns, 100mM CaCl2.
Trajectory originally donated to SlimMD

# data[].attributes.title
DNA Minicircle (339 base pairs) with 30 turns 30ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes._psdi_force_fields
AMBER99 for DNA, parmBSC0, parmOL4, parmOL1 corrections for backbone dihedrals, TIP3P water.

# data[].attributes.annote
Classical MD simulations of the P2Y1 receptor bound to BPTU in the water-POPC bilayer. 0.15M of Na+ and Cl-. Three replicates are provided. 
Trajectory originally donated to SlimMD

# data[].attributes.title
P2Y1 purinergic receptor bound to BPTU the allosteric modulator 40 ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
Probe MD simulations. Mapping an allosteric site at the lipid interface of the P2Y1 purinergic receptor. The P2Y1 receptor in the presence of 10% of 2-hydroxypyridine (P2O) in the water-POPC bilayer. 0.15M of Na+ and Cl-. Three replicates are provided. 
Trajectory originally donated to SlimMD

# data[].attributes.title
P2Y1 purinergic receptor in the presence of 10% of 2-hydroxypyridine (P2O) 40ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
DNA minicircle (339 base pairs) with 31 turns 30ns, 100mM CaCl2.
Trajectory originally donated to SlimMD

# data[].attributes.title
DNA minicircle (339 base pairs) with 31 turns 30ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes._psdi_force_fields
AMBER99 for DNA, parmBSC0, parmOL4, parmOL1 corrections for backbone dihedrals, TIP3P water.

# data[].attributes.annote
A trio of trajectories are supplied whose data was published in Sahai, M.A. et. al. 2017. They include the human dopamine transporter (hDAT), imbedded in a membrane, bound to amphetamine, MDMA and the new psychoactive substance (NPS) 5-MAPB. In VMD the segid for these compounds are AMP, MDMA and MAPB, respectively, If you align all three trajectories on the protein backbone they can be compared with respect to destabilisation of the second sodium NA2 in the binding site. Residues of importance can be found in Fig 5 and 6 of the attached paper. Any questions please direct them to Michelle Sahai: michelle.sahai@roehampton.ac.uk.
Monovalent neutralising ionic environment. 
Trajectory originally donated to SlimMD

# data[].attributes.title
Human dopamine transporter embedded in a membrane, bound to MDMA 250ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes._psdi_force_fields
CHARMM27 (protein), CHARMM36 (lipids), TIP3P (water)

# data[].attributes.annote
Probe MD simulations. Mapping an allosteric site at the intracellular side of the Beta2 adrenergic receptor. Beta2 adrenergic receptor in the presence of 10% of benzamide (BZA) in the water-POPC bilayer. 0.15M of Na+ and Cl-. Three replicates are provided. 
Trajectory originally donated to SlimMD

# data[].attributes.title
Beta2 adrenergic receptor in the presence of 10% of benzamide (BZA) 40 ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
DNA minicircle (339 base pairs) with 29 turns 30ns, 100mM CaCl2.
Trajectory originally donated to SlimMD

# data[].attributes.title
DNA minicircle (339 base pairs) with 29 turns 30ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes._psdi_force_fields
AMBER99 for DNA, parmBSC0, parmOL4, parmOL1 corrections for backbone dihedrals, TIP3P water.

# data[].attributes.annote
Classical MD simulations. M2 muscarinic receptor bound to Iperoxo agonist and LY2119620 allosteric modulator in the water-POPC bilayer. 0.15 M of Na+ and Cl-
Trajectory originally donated to SlimMD

# data[].attributes.title
M2 muscarinic receptor bound to Iperoxo agonist and LY2119620 allosteric modulator 40 ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
M2 muscarinic receptor bound to Iperoxo agonist (LIG) in the presence of 10 % Thieno[2,3-b]pyridine (THP). The system in the water-POPC bilayer. 0.15M Na+ and Cl- ions.
Trajectory originally donated to SlimMD

# data[].attributes.title
M2 muscarinic receptor bound to Iperoxo agonist in the presence of 10% THP 40 ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
A trio of trajectories are supplied whose data was published in Sahai, M.A. et. al. 2017. They include the human dopamine transporter (hDAT), imbedded in a membrane, bound to amphetamine, MDMA and the new psychoactive substance (NPS) 5-MAPB. In VMD the segid for these compounds are AMP, MDMA and MAPB, respectively, If you align all three trajectories on the protein backbone they can be compared with respect to destabilisation of the second sodium NA2 in the binding site. Residues of importance can be found in Fig 5 and 6 of the attached paper. Any questions please direct them to Michelle Sahai: michelle.sahai@roehampton.ac.uk. 
Monovalent neutralising ionic environment. 
Trajectory originally donated to SlimMD

# data[].attributes.title
Human dopamine transporter embedded in a membrane, bound to amphetamine  250ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes._psdi_force_fields
CHARMM27 (protein), CHARMM36 (lipids), TIP3P (water)

# data[].attributes.annote
Classical MD simulations of the Beta2 adrenergic receptor in the empty form in the water-POPC bilayer. 0.15 M of Na+ and Cl-. Three replicates. 
Trajectory originally donated to SlimMD

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
Classical MD simulations of the Beta2 adrenergic receptor bound to Cmp-15 in the water-POPC bilayer. 0.15M of Na+ and Cl-. Three replicates are provided. 
Trajectory originally donated to SlimMD

# data[].attributes.title
Beta2 adrenergic receptor bound to Cmp-15 40 ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
A trio of trajectories are supplied whose data was published in Sahai, M.A. et. al. 2017. They include the human dopamine transporter (hDAT), imbedded in a membrane, bound to amphetamine, MDMA and the new psychoactive substance (NPS) 5-MAPB. In VMD the segid for these compounds are AMP, MDMA and MAPB, respectively, If you align all three trajectories on the protein backbone they can be compared with respect to destabilisation of the second sodium NA2 in the binding site. Residues of importance can be found in Fig 5 and 6 of the attached paper. Any questions please direct them to Michelle Sahai: michelle.sahai@roehampton.ac.uk
Monovalent neutralising ionic environment. 
Trajectory originally donated to SlimMD

# data[].attributes.title
Human dopamine transporter embedded in a membrane, bound to novel psychoactive substance MAPB 250ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes._psdi_force_fields
CHARMM27 (protein), CHARMM36 (lipids), TIP3P (water)

# data[].attributes.annote
Classical MD simulations. The M2 muscarinic receptor empty form in the water-POPC bilayer. 0.15 M of Na+ and Cl-. Three replicates are provided.
Trajectory originally donated to SlimMD

# data[].attributes.title
M2 muscarinic receptor in the empty form 40 ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
Example setup of a martini2 coarse-grained molecular dynamics simulation of the active state PTH2R (Parathyroid hormone receptor type 2) protein embedded in a lipid bilayer membrane along with water and counter-ions. Command-line tools provided in aiida-gromacs are used to track each step performed on the terminal.
 
The data:
The files in this record are:
1144.dot.pdf: The image of the graph representation for the simulation workflow.
gpcr_all_steps.aiida: The aiida archive file where all simulation setup steps performed in this work are packaged.
 
The stripped trajectory for the active and inactive states of PTH2R are in the following files:
R1a.pdb and R1a.xtc: pdb and trajectory of coordinates for the active state protein.
R1i.pdb and R1i.xtc pdb and trajectory of coordinates for the inactive state protein.

# data[].attributes.title
Coarse-grained MD simulation provenance of membrane embedded GPCR using GROMACS and aiida-gromacs

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
Classical MD simulations of the P2Y1 receptor in the empty form in the in the water-POPC bilayer. 0.15M of Na+ and Cl-. Three replicates are provided. 
Trajectory originally donated to SlimMD

# data[].attributes.title
P2Y1 purinergic receptor in the empty form 40 ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
Probe MD simulations. M2 muscarinic receptor bound to Iperoxo agonist in the presence of 10 % N-methylformamide (NMF) in the water-POPC bilayer. 0.15 M of Na+ and Cl-. Three replicates of simulations are provided.
Trajectory originally donated to SlimMD

# data[].attributes.title
M2 muscarinic receptor bound to Iperoxo agonist in the presence of 10% NMF 40 ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes.annote
DNA minicircle (339 base pairs) with 26 turns 30ns, 100mM CaCl2.
Trajectory originally donated to SlimMD

# data[].attributes.title
DNA minicircle (339 base pairs) with 26 turns 30ns

# data[].attributes._psdi_rights[]
Creative Commons Attribution 4.0 International

# data[].attributes._psdi_force_fields
AMBER99 for DNA, parmBSC0, parmOL4, parmOL1 corrections for backbone dihedrals, TIP3P water.

# meta.provider.name
Physical Sciences Data Infrastructure (PSDI)

# meta.provider.description
The Physical Sciences Data Infrastructure (PSDI) is an integrated data infrastructure that directly supports researchers in the physical sciences in the UK to manage, transform and share their data led by the Science and Technology Facilities Council (STFC) and the University of Southampton. As part of this ecosystem, PSDI serves as an OPTIMADE provider to make some data sources available via OPTIMADE endpoints.