diff --git a/NAMD/Tutorial-1.html b/NAMD/Tutorial-1.html index 84d8319..8ccf78e 100644 --- a/NAMD/Tutorial-1.html +++ b/NAMD/Tutorial-1.html @@ -244,7 +244,7 @@

1.4. Create Backbone and Protein restraints
vmd -dispdev text –e restraints.tcl
+
vmd -dispdev text -e restraints.tcl
 

 

 
@@ -257,7 +257,7 @@ 
1.5.1 NAMD2

Copy the input files to the folder:

-
cp sirah.amber/tutorial/NAMD/1/NAMD2/*.conf .
+
cp ../sirah.amber/tutorial/NAMD/1/NAMD2/*.conf .
 

 

 
The folder sirah.amber/tutorial/NAMD/1/NAMD2 contains typical input files for energy minimization (em1.conf and em2.conf), heating (heat.conf), equilibration (eq1.conf and eq2.conf) and production (md.conf) runs.  Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.

@@ -319,12 +319,16 @@ 
1.5.1 NAMD2
 
 

 
1.5.2 NAMD3

+

+
Warning

+
Point release 3.0.1 fixes potentially impactful bugs in 3.0. All users are strongly encouraged to upgrade to this version.

+

 
Make a new folder for the run:

 
mkdir -p run; cd run
 

 

 
Copy the input files to the folder:

-
cp sirah.amber/tutorial/NAMD/1/NAMD3/*.conf .
+
cp ../sirah.amber/tutorial/NAMD/1/NAMD3/*.conf .
 

 

 
The folder sirah.amber/tutorial/NAMD/1/NAMD3 contains typical input files for energy minimization (em1.conf and em2.conf), heating (heat.conf), equilibration (eq1.conf and eq2.conf) and production (md.conf) runs.  Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.

@@ -532,7 +536,7 @@ 
1.7.4 Equilibration
# Constraints of protein
 if {1} {                                   ;# If 1 read the block
 constraints           on                   ;# Turns on constraints
-consref               your_restraints.pdb  ;# Reference PDB file for constraint positions
+consref               your_restraints.coor  ;# Reference PDB file for the last position (last_step.coor)
 conskfile             your_restraints.pdb  ;# File containing constraint force constants
 constraintScaling     1                    ;# Scaling factor for constraint forces
 consexp               2                    ;# Exponent for constraint potential
@@ -547,7 +551,7 @@ 
1.7.4 Equilibration
# Constraints of protein
 if {1} {                                   ;# If 1 read the block
 constraints           on                   ;# Turns on constraints
-consref               your_restraints.pdb  ;# Reference PDB file for constraint positions
+consref               your_restraints.coor  ;# Reference PDB file for the last position (last_step.coor)
 conskfile             your_restraints.pdb  ;# File containing constraint force constants
 constraintScaling     0.1                  ;# Scaling factor for constraint forces
 consexp               2                    ;# Exponent for constraint potential
diff --git a/Tutorials namd.html b/Tutorials namd.html
index 40eef4e..9ac8a33 100644
--- a/Tutorials namd.html	
+++ b/Tutorials namd.html	
@@ -359,7 +359,7 @@ 
1.4. Create Backbone and Protein restraints
vmd -dispdev text –e restraints.tcl
+
vmd -dispdev text -e restraints.tcl
 

 

 

@@ -372,7 +372,7 @@ 
1.5.1 NAMD2

Copy the input files to the folder:

-
cp sirah.amber/tutorial/NAMD/1/NAMD2/*.conf .
+
cp ../sirah.amber/tutorial/NAMD/1/NAMD2/*.conf .
 

 

 
The folder sirah.amber/tutorial/NAMD/1/NAMD2 contains typical input files for energy minimization (em1.conf and em2.conf), heating (heat.conf), equilibration (eq1.conf and eq2.conf) and production (md.conf) runs.  Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.

@@ -434,12 +434,16 @@ 
1.5.1 NAMD2
 
 

 
1.5.2 NAMD3

+

+
Warning

+
Point release 3.0.1 fixes potentially impactful bugs in 3.0. All users are strongly encouraged to upgrade to this version.

+

 
Make a new folder for the run:

 
mkdir -p run; cd run
 

 

 
Copy the input files to the folder:

-
cp sirah.amber/tutorial/NAMD/1/NAMD3/*.conf .
+
cp ../sirah.amber/tutorial/NAMD/1/NAMD3/*.conf .
 

 

 
The folder sirah.amber/tutorial/NAMD/1/NAMD3 contains typical input files for energy minimization (em1.conf and em2.conf), heating (heat.conf), equilibration (eq1.conf and eq2.conf) and production (md.conf) runs.  Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.

@@ -647,7 +651,7 @@ 
1.7.4 Equilibration
# Constraints of protein
 if {1} {                                   ;# If 1 read the block
 constraints           on                   ;# Turns on constraints
-consref               your_restraints.pdb  ;# Reference PDB file for constraint positions
+consref               your_restraints.coor  ;# Reference PDB file for the last position (last_step.coor)
 conskfile             your_restraints.pdb  ;# File containing constraint force constants
 constraintScaling     1                    ;# Scaling factor for constraint forces
 consexp               2                    ;# Exponent for constraint potential
@@ -662,7 +666,7 @@ 
1.7.4 Equilibration
# Constraints of protein
 if {1} {                                   ;# If 1 read the block
 constraints           on                   ;# Turns on constraints
-consref               your_restraints.pdb  ;# Reference PDB file for constraint positions
+consref               your_restraints.coor  ;# Reference PDB file for the last position (last_step.coor)
 conskfile             your_restraints.pdb  ;# File containing constraint force constants
 constraintScaling     0.1                  ;# Scaling factor for constraint forces
 consexp               2                    ;# Exponent for constraint potential
diff --git a/_sources/NAMD/Tutorial-1.rst.txt b/_sources/NAMD/Tutorial-1.rst.txt
index 7182b3f..6581419 100644
--- a/_sources/NAMD/Tutorial-1.rst.txt
+++ b/_sources/NAMD/Tutorial-1.rst.txt
@@ -199,7 +199,7 @@ Run the VMD script to generate the pdb restriction file:
 
 .. code-block:: bash
 
-    vmd -dispdev text –e restraints.tcl 
+    vmd -dispdev text -e restraints.tcl 
 
 
 1.5. Run the simulation
@@ -218,7 +218,7 @@ Copy the input files to the folder:
 
 .. code-block:: bash
 
-    cp sirah.amber/tutorial/NAMD/1/NAMD2/*.conf .
+    cp ../sirah.amber/tutorial/NAMD/1/NAMD2/*.conf .
 
 The folder ``sirah.amber/tutorial/NAMD/1/NAMD2`` contains typical input files for energy minimization (``em1.conf`` and ``em2.conf``), heating (``heat.conf``), equilibration (``eq1.conf`` and ``eq2.conf``) and production (``md.conf``) runs.  Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.
 
@@ -300,6 +300,10 @@ The folder ``sirah.amber/tutorial/NAMD/1/NAMD2`` contains typical input files fo
 1.5.2 NAMD3
 ~~~~~~~~~~~~~
 
+.. warning::
+
+    Point release 3.0.1 fixes potentially impactful bugs in 3.0. All users are strongly encouraged to upgrade to this version.
+
 Make a new folder for the run:
 
 .. code-block:: bash
@@ -310,7 +314,7 @@ Copy the input files to the folder:
 
 .. code-block:: bash
 
-    cp sirah.amber/tutorial/NAMD/1/NAMD3/*.conf .
+    cp ../sirah.amber/tutorial/NAMD/1/NAMD3/*.conf .
 
 The folder ``sirah.amber/tutorial/NAMD/1/NAMD3`` contains typical input files for energy minimization (``em1.conf`` and ``em2.conf``), heating (``heat.conf``), equilibration (``eq1.conf`` and ``eq2.conf``) and production (``md.conf``) runs.  Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.
 
@@ -559,7 +563,7 @@ For ``eq1.conf``:
     # Constraints of protein 
     if {1} {                                   ;# If 1 read the block 
     constraints           on                   ;# Turns on constraints 
-    consref               your_restraints.pdb  ;# Reference PDB file for constraint positions 
+    consref               your_restraints.coor  ;# Reference PDB file for the last position (last_step.coor) 
     conskfile             your_restraints.pdb  ;# File containing constraint force constants 
     constraintScaling     1                    ;# Scaling factor for constraint forces 
     consexp               2                    ;# Exponent for constraint potential 
@@ -577,7 +581,7 @@ For ``eq2.conf``:
     # Constraints of protein 
     if {1} {                                   ;# If 1 read the block 
     constraints           on                   ;# Turns on constraints 
-    consref               your_restraints.pdb  ;# Reference PDB file for constraint positions 
+    consref               your_restraints.coor  ;# Reference PDB file for the last position (last_step.coor)
     conskfile             your_restraints.pdb  ;# File containing constraint force constants 
     constraintScaling     0.1                  ;# Scaling factor for constraint forces 
     consexp               2                    ;# Exponent for constraint potential 
diff --git a/_static/js/versions.js b/_static/js/versions.js
index 818bc99..4958195 100644
--- a/_static/js/versions.js
+++ b/_static/js/versions.js
@@ -1,6 +1,6 @@
 const themeFlyoutDisplay = "hidden";
-const themeVersionSelector = "True";
-const themeLanguageSelector = "True";
+const themeVersionSelector = true;
+const themeLanguageSelector = true;
 
 if (themeFlyoutDisplay === "attached") {
   function renderLanguages(config) {
@@ -8,10 +8,14 @@ if (themeFlyoutDisplay === "attached") {
       return "";
     }
 
+    // Insert the current language to the options on the selector
+    let languages = config.projects.translations.concat(config.projects.current);
+    languages = languages.sort((a, b) => a.language.name.localeCompare(b.language.name));
+
     const languagesHTML = `
       

         
Languages

-        ${config.projects.translations
+        ${languages
           .map(
             (translation) => `
         

diff --git a/searchindex.js b/searchindex.js
index 65ac3f3..ef4f7a2 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1. DNA molecule in explicit solvent": [[32, "dna-molecule-in-explicit-solvent"]], "1. DNA molecule in implicit solvent": [[30, "dna-molecule-in-implicit-solvent"]], "1. Proteins in explicit solvent": [[33, "proteins-in-explicit-solvent"]], "1.1 RMSD Visualizer Tool": [[12, "rmsd-visualizer-tool"], [31, "rmsd-visualizer-tool"]], "1.1. Build CG representations": [[1, null], [18, null], [27, null], [30, "build-cg-representations"], [32, "build-cg-representations"], [33, "build-cg-representations"]], "1.2. PDB to GROMACS format": [[18, "pdb-to-gromacs-format"], [32, "pdb-to-gromacs-format"]], "1.2. Prepare LEaP input": [[1, "prepare-leap-input"], [30, "prepare-leap-input"]], "1.2. Prepare with LEaP": [[27, "prepare-with-leap"], [33, "prepare-with-leap"]], "1.2. Tcl script": [[12, "tcl-script"], [31, "tcl-script"]], "1.3. Run LEaP": [[1, "run-leap"], [27, "run-leap"], [30, "run-leap"], [33, "run-leap"]], "1.3. Solvate the system": [[18, "solvate-the-system"], [32, "solvate-the-system"]], "1.4. Create Backbone and Protein restraints": [[27, "create-backbone-and-protein-restraints"], [33, "create-backbone-and-protein-restraints"]], "1.4. Run the simulation": [[1, "run-the-simulation"], [18, "run-the-simulation"], [30, "run-the-simulation"], [32, "run-the-simulation"]], "1.5. Run the simulation": [[27, "run-the-simulation"], [33, "run-the-simulation"]], "1.5. Visualizing the simulation": [[1, "visualizing-the-simulation"], [18, "visualizing-the-simulation"], [30, "visualizing-the-simulation"], [32, "visualizing-the-simulation"]], "1.5.1 NAMD2": [[27, "namd2"], [33, "namd2"]], "1.5.2 NAMD3": [[27, "namd3"], [33, "namd3"]], "1.6. Visualizing the simulation": [[27, "visualizing-the-simulation"], [33, "visualizing-the-simulation"]], "1.7 How to modify input files": [[27, "how-to-modify-input-files"], [33, "how-to-modify-input-files"]], "1.7.1 All files": [[27, "all-files"], [33, "all-files"]], "1.7.2 Energy minimization": [[27, "energy-minimization"], [33, "energy-minimization"]], "1.7.3 Heating": [[27, "heating"], [33, "heating"]], "1.7.4 Equilibration": [[27, "equilibration"], [33, "equilibration"]], "1.7.5 Production": [[27, "production"], [33, "production"]], "2. DNA molecule in explicit solvent": [[30, "dna-molecule-in-explicit-solvent"]], "2. Hybrid solvation": [[32, "hybrid-solvation"]], "2.1. Build CG representations": [[2, null], [30, "id12"]], "2.1. PDB to GROMACS format": [[19, null], [32, "id9"]], "2.2. Prepare LEaP input": [[2, "prepare-leap-input"], [30, "id13"]], "2.2. Solvate the system": [[19, "solvate-the-system"], [32, "id10"]], "2.3. Run LEaP": [[2, "run-leap"], [30, "id14"]], "2.3. Run the simulation": [[19, "run-the-simulation"], [32, "id11"]], "2.4. Run the simulation": [[2, "run-the-simulation"], [30, "id15"]], "2.4. Visualizing the simulation": [[19, "visualizing-the-simulation"], [32, "id12"]], "2.5. Visualizing the simulation": [[2, "visualizing-the-simulation"], [30, "id16"]], "3. Multiscale simulation in implicit solvent": [[30, "multiscale-simulation-in-implicit-solvent"]], "3. Proteins in explicit solvent": [[32, "proteins-in-explicit-solvent"]], "3.1. Build CG representations": [[3, null], [20, null], [30, "id19"], [32, "id17"]], "3.2. PDB to GROMACS format": [[20, "pdb-to-gromacs-format"], [32, "id19"]], "3.2. Prepare LEaP input": [[3, "prepare-leap-input"], [30, "id20"]], "3.3. Run LEaP": [[3, "run-leap"], [30, "id21"]], "3.3. Solvate the system": [[20, "solvate-the-system"], [32, "id20"]], "3.4. Run the simulation": [[3, "run-the-simulation"], [20, "run-the-simulation"], [30, "id22"], [32, "id22"]], "3.5. Visualizing the simulation": [[3, "visualizing-the-simulation"], [20, "visualizing-the-simulation"], [30, "id23"], [32, "id23"]], "4. Closed circular DNA in explicit solvent": [[32, "closed-circular-dna-in-explicit-solvent"]], "4. Closed circular DNA in implicit solvent": [[30, "closed-circular-dna-in-implicit-solvent"]], "4.1. Build CG representations": [[4, null], [21, null], [30, "id29"], [32, "id29"]], "4.2. PDB to GROMACS format": [[21, "pdb-to-gromacs-format"], [32, "id30"]], "4.2. Prepare LEaP input": [[4, "prepare-leap-input"], [30, "id30"]], "4.3. Run LEaP": [[4, "run-leap"], [30, "id31"]], "4.3. Solvate the system": [[21, "solvate-the-system"], [32, "id31"]], "4.4. Run the simulation": [[4, "run-the-simulation"], [21, "run-the-simulation"], [30, "id32"], [32, "id33"]], "4.5. Visualizing the simulation": [[4, "visualizing-the-simulation"], [21, "visualizing-the-simulation"], [30, "id33"], [32, "id34"]], "5. Lipid bilayers in explicit solvent": [[32, "lipid-bilayers-in-explicit-solvent"]], "5. Proteins in explicit solvent": [[30, "proteins-in-explicit-solvent"]], "5.1. Build CG representations": [[5, null], [22, null], [30, "id37"], [32, "id38"]], "5.2. PDB to GROMACS format": [[22, "pdb-to-gromacs-format"], [32, "id39"]], "5.2. Prepare LEaP input": [[5, "prepare-leap-input"], [30, "id39"]], "5.3. Run LEaP": [[5, "run-leap"], [30, "id40"]], "5.3. Solvate the system": [[22, "solvate-the-system"], [32, "id40"]], "5.4. Run the simulation": [[5, "run-the-simulation"], [22, "run-the-simulation"], [30, "id41"], [32, "id42"]], "5.5. Visualizing the simulation": [[5, "visualizing-the-simulation"], [22, "visualizing-the-simulation"], [30, "id42"], [32, "id43"]], "6. Lipid bilayers in explicit solvent": [[30, "lipid-bilayers-in-explicit-solvent"]], "6. Membrane proteins in explicit solvent": [[32, "membrane-proteins-in-explicit-solvent"]], "6.1. Build CG representations": [[6, null], [23, null], [30, "id46"], [32, "id48"]], "6.1.1. Embed the protein in a lipid bilayer": [[23, "embed-the-protein-in-a-lipid-bilayer"], [32, "embed-the-protein-in-a-lipid-bilayer"]], "6.1.2. Delete close contact lipid molecules": [[23, "delete-close-contact-lipid-molecules"], [32, "delete-close-contact-lipid-molecules"]], "6.2. PDB to GROMACS format": [[23, "pdb-to-gromacs-format"], [32, "id51"]], "6.2. Prepare LEaP input": [[6, "prepare-leap-input"], [30, "id47"]], "6.3. Run LEaP": [[6, "run-leap"], [30, "id49"]], "6.3. Solvate the system": [[23, "solvate-the-system"], [32, "id52"]], "6.4. Generate position restraint files": [[23, "generate-position-restraint-files"], [32, "generate-position-restraint-files"]], "6.4. Resize the box with CPPTRAJ": [[6, "resize-the-box-with-cpptraj"], [30, "resize-the-box-with-cpptraj"]], "6.5. Run the simulation": [[6, "run-the-simulation"], [23, "run-the-simulation"], [30, "id50"], [32, "id54"]], "6.6. Visualizing the simulation": [[6, "visualizing-the-simulation"], [23, "visualizing-the-simulation"], [30, "id51"], [32, "id55"]], "7. Membrane proteins in explicit solvent": [[30, "membrane-proteins-in-explicit-solvent"]], "7. SMD with multiscale solvent": [[32, "smd-with-multiscale-solvent"]], "7.1. Build CG representations": [[7, null], [30, "id56"]], "7.1. Setting pulling direction": [[24, null], [32, "setting-pulling-direction"]], "7.1.1. Embed the protein in a lipid bilayer": [[7, "embed-the-protein-in-a-lipid-bilayer"], [30, "embed-the-protein-in-a-lipid-bilayer"]], "7.1.2. Delete close contact lipid molecules": [[7, "delete-close-contact-lipid-molecules"], [30, "delete-close-contact-lipid-molecules"]], "7.2. Build CG representations": [[24, "build-cg-representations"], [32, "id59"]], "7.2. Prepare LEaP input": [[7, "prepare-leap-input"], [30, "id58"]], "7.3. PDB to GROMACS format": [[24, "pdb-to-gromacs-format"], [32, "id62"]], "7.3. Run LEaP": [[7, "run-leap"], [30, "id59"]], "7.4. Resize the box with CPPTRAJ": [[7, "resize-the-box-with-cpptraj"], [30, "id61"]], "7.4. Solvate the system": [[24, "solvate-the-system"], [32, "id63"]], "7.5. Run the simulation": [[7, "run-the-simulation"], [24, "run-the-simulation"], [30, "id62"], [32, "id65"]], "7.6. Visualizing the simulation": [[7, "visualizing-the-simulation"], [24, "visualizing-the-simulation"], [30, "id63"], [32, "id66"]], "8. Glycoprotein in explicit solvent": [[30, "glycoprotein-in-explicit-solvent"]], "8.1. Build CG representations": [[8, null], [30, "id68"]], "8.2. Prepare LEaP input": [[8, "prepare-leap-input"], [30, "id71"]], "8.3. Run LEaP": [[8, "run-leap"], [30, "id72"]], "8.4. Run the simulation": [[8, "run-the-simulation"], [30, "id73"]], "8.5. Visualizing the simulation": [[8, "visualizing-the-simulation"], [30, "id74"]], "9. Non-enveloped Viral-Like Particle": [[30, "non-enveloped-viral-like-particle"]], "9.1. Structure preprocessing": [[9, null], [30, "structure-preprocessing"]], "9.1.1 Working with the Biological Assembly of an entire VLP": [[9, "working-with-the-biological-assembly-of-an-entire-vlp"], [30, "working-with-the-biological-assembly-of-an-entire-vlp"]], "9.1.2 Calculate system charge": [[9, "calculate-system-charge"], [30, "calculate-system-charge"]], "9.1.3 Packing the assimetric unit to build an entire VLP (Alternative)": [[9, "packing-the-assimetric-unit-to-build-an-entire-vlp-alternative"], [30, "packing-the-assimetric-unit-to-build-an-entire-vlp-alternative"]], "9.2. Build CG representations": [[9, "build-cg-representations"], [30, "id82"]], "9.3. Wrapping up VLP system with Packmol": [[9, "wrapping-up-vlp-system-with-packmol"], [30, "wrapping-up-vlp-system-with-packmol"]], "9.4 Prepare LEaP input": [[9, "prepare-leap-input"], [30, "id83"]], "9.5 Run LEaP": [[9, "run-leap"], [30, "id84"]], "9.6. Run the simulation": [[9, "run-the-simulation"], [30, "id85"]], "9.7. Visualizing the simulation": [[9, "visualizing-the-simulation"], [30, "id86"]], "AMBER": [[30, null]], "AMBER questions": [[16, "amber-questions"]], "About SIRAH": [[11, null]], "Acknowledgments": [[11, "acknowledgments"]], "Advantages": [[11, "advantages"]], "Appendix": [[30, "appendix"]], "Available mapping files": [[0, "available-mapping-files"], [30, "available-mapping-files"]], "Background": [[13, null]], "Backmapping analysis": [[29, "backmapping-analysis"], [34, "backmapping-analysis"]], "Basic analyses VMD": [[31, null]], "Calculating ionic concentrations": [[0, null], [30, "calculating-ionic-concentrations"]], "Citations": [[14, null]], "DNA model": [[13, "dna-model"]], "Developers": [[15, null], [15, "id1"]], "Divalent cations": [[13, "divalent-cations"]], "Download and Setting up SIRAH": [[10, "download-and-setting-up-sirah"], [28, "download-and-setting-up-sirah"], [30, "download-and-setting-up-sirah"], [33, "download-and-setting-up-sirah"]], "Download and setting SIRAH": 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28, 29, 30, 33, 34], "ambermd": [29, 34], "ambertool": [8, 9, 10, 27, 28, 29, 30, 33, 34], "ambigu": [5, 8, 9, 16, 20, 27, 30, 32, 33], "ambpdb": [8, 30], "amelior": 16, "american": 16, "amid": [5, 8, 9, 16, 27, 30, 33], "amino": [9, 13, 16, 24, 29, 30, 32, 34], "aminoacid": 16, "among": [11, 35], "an": [3, 5, 6, 7, 8, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 31, 32, 33, 34], "anal": [1, 3, 4, 29, 30, 34], "analys": 12, "analysi": [12, 31], "analyz": [2, 5, 6, 7, 8, 9, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "andr": 15, "angl": [12, 29, 31, 34], "angletyp": [12, 29, 31, 34], "angstrom": [6, 7, 9, 22, 29, 30, 32, 34], "ani": [5, 7, 8, 9, 12, 16, 19, 20, 23, 24, 27, 29, 30, 31, 32, 33, 34], "anim": [29, 34], "anoth": [9, 12, 13, 14, 16, 25, 30, 31, 32], "answer": 16, "antibodi": 13, "anticip": [29, 34], "antonella": 15, "apl_dmpc64_310k": [6, 30], "appear": [9, 12, 16, 24, 29, 30, 31, 32, 34], "append": [6, 7, 12, 16, 22, 23, 29, 30, 31, 32, 34], "appendix": [2, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 32, 33], "appli": [3, 6, 7, 8, 13, 16, 18, 19, 22, 23, 24, 29, 30, 32, 34], "applic": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 14, 27, 29, 30, 31, 33, 34], "approach": [3, 9, 11, 13, 14, 19, 24, 30, 32, 35], "approxim": [6, 9, 13, 22, 30, 32], "aqua": [29, 34], "aqueou": [11, 13, 14, 17, 35], "ar": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35], "ara\u00fajo": [13, 17], "arbitrari": 11, "area": [6, 12, 22, 27, 30, 31, 32, 33], "area_lipid": [6, 30], "arg": [9, 30], "argentina": 16, "argument": [29, 34], "ari": 15, "aris": [12, 16, 31], "aromat": 13, "around": [9, 16, 24, 30, 32], "arrai": [29, 34], "artefactu": 16, "articl": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 18, 19, 20, 21, 22, 23, 27, 29, 30, 31, 32, 33, 34], "artifact": [9, 30], "artifactu": [16, 29, 34], "ascii": [12, 29, 31, 34], "ash": [5, 8, 9, 16, 20, 27, 30, 32, 33], "asn": [8, 30], "asp": [9, 30], "asp320": 16, "aspart": [5, 8, 9, 16, 20, 27, 30, 32, 33], "aspect": [12, 31], "assembl": [9, 13, 30], "assembli": 17, "assembly1": [9, 30], "assess": [12, 17, 31], "assign": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "associ": 13, "astrid": 15, "asymetr": [9, 30], "asymmetr": [9, 16, 30], "ataxia": 17, "atom": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34, 35], "atomist": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35], "atomselect": [12, 24, 27, 31, 32, 33], "atpas": 17, "attempt": [9, 30], "attent": [5, 8, 9, 20, 27, 30, 32, 33], "auto": [25, 32], "autoimag": [2, 5, 6, 7, 8, 30], "autoinhibit": 17, "automat": [9, 16, 18, 19, 20, 21, 22, 23, 24, 30, 32], "avail": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34], "averag": [12, 29, 31, 34], "avoid": [1, 2, 3, 6, 7, 16, 18, 22, 23, 29, 30, 32, 34], "avx": [12, 29, 31, 34], "avx2": [12, 29, 31, 34], "aw3": [4, 30], "aw5": [4, 21, 30, 32], "awai": [5, 8, 9, 16, 27, 30, 33], "awar": [5, 8, 9, 16, 19, 20, 23, 24, 27, 29, 30, 32, 33, 34], "awk": [9, 30], "axi": [6, 16, 22, 24, 29, 30, 32, 34], "b": [3, 4, 12, 17, 21, 27, 29, 30, 31, 32, 33, 34], "baaden": 17, "back": [5, 8, 9, 16, 18, 20, 21, 22, 23, 24, 27, 30, 32, 33], "backbon": [5, 7, 8, 9, 12, 13, 16, 20, 23, 24, 29, 30, 31, 32, 34], "backmap": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "backmap_less_min": [29, 34], "bad": [6, 7, 16, 22, 30, 32], "balanc": [9, 30], "ballestero": [13, 14, 15, 17], "bar": [27, 33], "barostat": [27, 33], "barrera": [6, 7, 13, 14, 15, 17, 22, 23, 30, 32], "base": [0, 1, 2, 3, 6, 7, 9, 10, 12, 13, 16, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34], "bash": [28, 33], "basi": [17, 29, 34], "basic": [1, 2, 3, 4, 5, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34], "bb": [27, 33], "bb_restraint": [27, 33], "bba": 17, "bc1": [22, 32], "bc13": [7, 30], "bc2": [22, 32], "bc23": [7, 30], "bct": [22, 32], "bct1": [7, 30], "bct2": [7, 30], "bead": [6, 8, 9, 12, 13, 16, 20, 22, 23, 24, 29, 30, 31, 32, 34], "beadi": [8, 30], "beadj": [8, 30], "becam": 16, "becaus": [16, 27, 33], "becom": 16, "been": [9, 11, 13, 16, 18, 19, 20, 21, 22, 30, 32], "befor": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "begin": 16, "behavior": [1, 2, 3, 16, 29, 30, 34], "behind": [16, 24, 32], "being": [16, 35], "bellow": [7, 23, 27, 30, 32, 33], "below": [9, 12, 29, 30, 31, 34], "bend": [13, 17], "benefici": [11, 14], "berger": [0, 30], "bertipaglia": 17, "besid": [29, 34], "best": [2, 5, 6, 7, 8, 9, 20, 23, 24, 27, 29, 30, 32, 33, 34], "beta": [27, 29, 33, 34], "between": [6, 7, 9, 12, 13, 16, 18, 22, 23, 24, 29, 30, 31, 32, 34], "beyond": [7, 30], "bfo": [6, 22, 23, 30, 32], "big": [12, 16, 31], "bigger": 16, "bilay": 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31, 32, 33, 34], "box_xi": [22, 32], "brandner": [14, 15, 17], "brazilian": 17, "break": 16, "breath": [13, 17], "bridg": [5, 9, 27, 30, 33], "brief": 17, "bring": [27, 33], "brini": 17, "bruno": [13, 17], "bsb": 17, "bsc0": [3, 30], "bsc1": [3, 30], "bsg": [5, 8, 9, 16, 27, 30, 33], "bt": [18, 19, 20, 21, 24, 32], "bubbl": [13, 16, 17], "buffer": [3, 30], "bug": [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "build": [10, 16, 25, 28], "built": [12, 29, 31, 34], "bulk": [17, 19, 24, 32], "bulkier": 13, "buratto": [13, 17], "button": [12, 29, 31, 34], "byfram": [29, 34], "byre": [29, 34], "c": [1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 34], "c1": 13, "c1x": [4, 30], "c5": 13, "c5x": [12, 29, 31, 34], "ca": [9, 30], "ca2": 17, "caballero": [13, 14], "calc_n": [9, 30], "calcium": 13, "calcul": [6, 12, 16, 22, 27, 29, 31, 32, 33, 34], "call": [1, 2, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "calmodulin": 17, "cal\u00ec": 17, "can": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "cantero": [27, 33], "cap": [1, 2, 3, 18, 30, 32], "capabl": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33, 35], "capsid": [9, 13, 30], "capsom": [9, 30], "captur": 11, "carafoli": 17, "carbon": [12, 13, 31], "card": [27, 33], "care": [16, 26], "carefulli": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "carlo": 15, "carrasco": [13, 14], "carrer": [13, 17], "carri": [16, 18, 20, 21, 22, 23, 24, 27, 32, 33], "casalla": [13, 14, 17], "case": [5, 7, 8, 9, 10, 12, 16, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34], "caspas": 17, "castro": 17, "cat": [5, 8, 9, 27, 30, 33], "catalysi": 16, "catalyst": 16, "cation": 14, "caus": 16, "caution": [6, 7, 16, 22, 23, 24, 30, 32], "caviti": 16, "cax": [29, 34], "ccdna": [4, 21, 30, 32], "ccdna_cg": [4, 21, 30, 32], "ccdna_cg_box": [21, 32], "ccdna_cg_em": [4, 21, 30, 32], "ccdna_cg_eq": [4, 21, 30, 32], "ccdna_cg_ion": [21, 32], "ccdna_cg_md": [4, 21, 30, 32], "ccdna_cg_md_pbc": [21, 32], "ccdna_cg_sol": [21, 32], "cd": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 30, 32, 33], "cdot": [0, 30], "celiac": 17, "cell": [27, 33], "cellbasisvector": [27, 33], "cellbasisvector1": [27, 33], "cellbasisvector2": [27, 33], "cellbasisvector3": [27, 33], "cellorigin": [27, 33], "cellular": 13, "center": [7, 9, 12, 16, 18, 19, 20, 21, 24, 30, 31, 32], "certain": [11, 18, 19, 20, 21, 22, 29, 32, 34], "certainli": 16, "cg": [11, 12, 13, 14, 16, 17, 19, 31, 35], "cgconv": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 20, 21, 22, 23, 24, 27, 29, 30, 32, 33, 34], "chain": [5, 7, 8, 9, 11, 13, 16, 18, 20, 23, 24, 27, 30, 32, 33, 35], "challeng": 11, "chang": [9, 10, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34], "channel": 13, "chapter": [6, 22, 30, 32], "characterist": [6, 7, 13, 30], "charg": [2, 5, 7, 8, 13, 16, 20, 23, 24, 27, 29, 32, 33, 34], "charmm": [0, 5, 7, 8, 9, 16, 19, 20, 23, 24, 26, 27, 30, 32, 33], "charmm_lipid": [0, 30], "check": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "chemic": [11, 13, 14, 17, 35], "chemistri": [17, 29, 34], "chirdo": 17, "chlorid": 13, "chngmask": [2, 5, 8, 9, 16, 30], "choic": [19, 32], "cholin": 13, "choos": [5, 7, 8, 9, 12, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "chose": [29, 34], "chosen": [19, 32], "cif": [9, 30], "circl": [21, 32], "circoviru": [9, 30], "circular": [4, 21], "circumv": [9, 30], "cite": [11, 14], "citiu": [13, 14], "ckp": [0, 30], "cl": [2, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "clash": [7, 9, 16, 30], "classic": 13, "classif": [29, 34], "classifi": [29, 34], "clean": [27, 29, 33, 34], "click": [7, 9, 12, 23, 29, 30, 31, 32, 34], "clip": [7, 23, 30, 32], "close": [2, 4, 5, 6, 8, 9, 12, 16, 19, 21, 27, 29, 31, 33, 34], "cluster": 16, "clw": [2, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 32, 33, 34], "cmm": [22, 23, 32], "coars": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34, 35], "code": [5, 6, 7, 8, 9, 11, 16, 23, 24, 26, 27, 29, 30, 32, 33, 34, 35], "coeffici": [27, 33], "cof": 11, "cohes": [7, 30], "coil": [16, 29, 34], "coincident": 16, "collaps": 16, "collect": [11, 13, 35], "color": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "column": [27, 33], "combin": [11, 16, 19, 29, 32, 34, 35], "come": [24, 32], "command": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "commandnam": [29, 34], "comment": [27, 33], "common": [9, 11, 12, 16, 26, 30, 31], "commonli": [1, 2, 3, 4, 5, 6, 7, 8, 9, 30], "commun": [11, 17, 35], "compact": [12, 18, 19, 20, 21, 24, 31, 32], "compar": [11, 12, 31, 35], "comparison": 26, "compart": [9, 30], "compat": [0, 5, 8, 9, 11, 12, 13, 16, 20, 23, 24, 27, 30, 31, 32, 33], "compens": [9, 30], "compil": [29, 34], "complain": [23, 24, 32], "complementar": 13, "complet": [7, 9, 12, 13, 23, 24, 30, 31, 32], "complex": [9, 11, 12, 13, 14, 17, 29, 30, 31, 34, 35], "compli": [9, 30], "compon": [12, 13, 29, 31, 34, 35], "compos": [1, 2, 3, 4, 6, 18, 21, 22, 30, 32], "compound": [18, 19, 20, 21, 22, 23, 24, 32], "comprehens": [9, 13, 30], "compromis": 16, "comput": [9, 10, 11, 12, 13, 14, 16, 17, 25, 28, 30, 31, 32, 33], "concaten": [7, 23, 30, 32], "concentr": [2, 5, 6, 7, 8, 9, 12, 18, 19, 20, 21, 22, 23, 24, 27, 31, 32, 33], "concern": 16, "conda": [9, 29, 30, 34], "condit": [2, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 34], "conduct": [9, 12, 13, 30, 31], "conf": [27, 33], "configur": [6, 13, 22, 27, 30, 32, 33], "conflict": [0, 16, 30], "conform": [11, 12, 16, 17, 24, 29, 31, 32, 34], "conjug": [29, 34], "conjunct": [12, 31], 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23, 24, 26, 29, 30, 32, 34], "coor": [27, 33], "coordin": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 23, 24, 27, 29, 30, 31, 32, 33, 34], "copi": [24, 27, 32, 33], "core": [9, 16, 27, 30, 33], "correct": [5, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 33, 34], "correctli": [9, 16, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 34], "correl": [27, 33], "correspond": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 30, 31, 32, 33], "cost": 13, "could": [16, 24, 29, 32, 34], "coulomb": 26, "count": [9, 30], "countcharg": [9, 30], "counterion": [2, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "coupl": [16, 29, 34], "cours": [1, 2, 3, 9, 30], "cov": 17, "coval": [4, 11, 13, 30, 35], "cover": [13, 29, 34], "cp": [18, 19, 20, 21, 22, 23, 24, 27, 32, 33], "cpk": [29, 34], "cpptraj": [2, 5, 8, 9, 16], "cpu": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 27, 29, 30, 31, 32, 33, 34], "crash": 16, "crate": [23, 32], "crd": 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14, 15, 17, 18, 19, 20, 21, 29, 30, 32, 34], "d1": 16, "d2": 16, "d6": 16, "dalk": [12, 29, 31, 34], "damag": 17, "damiano": 17, "damp": [27, 33], "dan": [1, 2, 4, 13, 14, 15, 16, 17, 18, 20, 21, 30, 32], "daniela": 15, "dark": [29, 34], "darkviolet": [29, 34], "darr\u00e9": [5, 8, 9, 13, 14, 15, 17, 18, 19, 20, 24, 27, 30, 32, 33], "dat": [6, 9, 10, 12, 16, 21, 23, 25, 28, 30, 31, 32, 33], "data": [9, 11, 12, 17, 29, 30, 31, 34], "databas": [7, 11, 16, 23, 30, 32], "dataset": 17, "dcd": [27, 33], "dcx": [4, 21, 30, 32], "de": [11, 17, 29, 34], "dec": [29, 34], "decai": [27, 33], "decomposit": [29, 34], "decompress": [9, 30], "dedic": [12, 31], "default": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "defect": 16, "deffnm": [18, 19, 20, 21, 22, 23, 24, 32], "defin": [5, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 29, 30, 31, 32, 33, 34], "definit": [1, 2, 3, 5, 8, 9, 10, 16, 19, 25, 28, 30, 32, 33], "deform": [16, 29, 34], "degre": 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12, 13, 14, 16, 17, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "dz": [27, 33], "e": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "each": [2, 3, 5, 6, 7, 8, 9, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "easili": 16, "echo": [2, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 30, 32], "edg": [13, 27, 33], "edit": [9, 18, 19, 20, 21, 22, 23, 24, 26, 29, 30, 32, 34], "editconf": [18, 19, 20, 21, 22, 23, 24, 32], "editor": [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 27, 30, 32, 33], "edr": [22, 32], "edu": [12, 29, 31, 34], "effect": [1, 2, 3, 13, 16, 18, 30, 32], "effici": [11, 35], "either": 16, "elast": 16, "electr": [13, 16, 17], "electrolyt": [2, 5, 6, 7, 8, 9, 13, 14, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "electropor": 16, "electrostat": [13, 14, 26, 29, 34], "element": [16, 29, 34], "elsewher": [29, 34], "em": [16, 18, 19, 21, 22, 32], "em1": [20, 23, 24, 27, 32, 33], "em1_cgliprot": [23, 32], "em1_cgprot": [20, 24, 32], "em1_prot": [7, 30], "em1_wt4": [5, 8, 30], "em2": [20, 23, 24, 27, 32, 33], "em2_cgliprot": [23, 32], "em2_cgprot": [20, 24, 32], "em2_prot": [7, 30], "em2_wt4": [5, 8, 30], "em3": [24, 32], "em3_cgprot": [24, 32], "em_cgdna": [18, 21, 32], "em_cglip": [22, 32], "em_cpu": [9, 30], "em_gb": [1, 30], "em_gbsa": [4, 30], "em_hyb": [3, 30], "em_hybsol": [19, 32], "em_lipid": [6, 30], "em_wt4": [2, 30], "email": [12, 29, 31, 34], "embed": [2, 7, 19, 23, 24, 30, 32], "embrac": [5, 30], "empir": 16, "emploi": [9, 13, 24, 28, 30, 32, 33], "empti": [8, 30], "enabl": [13, 27, 33], "enantioselect": 16, "enclos": [24, 32], "encompass": 11, "end": [1, 2, 3, 4, 9, 18, 21, 22, 24, 27, 30, 32, 33], "endif": [18, 20, 23, 24, 32], "energi": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 19, 20, 21, 22, 23, 24, 26, 30, 32], "engin": [13, 16], "enhanc": [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "enough": [16, 24, 32], "ensembl": [11, 16, 35], "ensur": [9, 11, 13, 30, 35], "entail": 13, "enter": [9, 12, 29, 30, 31, 34], "entir": [7, 11, 13, 23, 29, 32, 34, 35], "entri": [29, 34], "enumer": [23, 32], "envelop": 9, "environ": [16, 29, 34], "epsilon": [5, 8, 9, 16, 20, 27, 30, 32, 33], "eq": [18, 19, 21, 22, 32], "eq1": [20, 23, 24, 27, 32, 33], "eq1_cgliprot": [23, 32], "eq1_cgprot": [20, 24, 32], "eq1_wt4": [5, 8, 30], "eq2": [20, 23, 24, 27, 32, 33], "eq2_cgliprot": [23, 32], "eq2_cgprot": [20, 24, 32], "eq2_wt4": [5, 8, 30], "eq_cgdna": [18, 21, 32], "eq_cglip": [22, 32], "eq_gb": [1, 2, 3, 30], "eq_gbsa": [4, 30], "eq_hyb": [3, 30], "eq_hybsol": [19, 32], "eq_lipid": [6, 30], "eq_prot": [7, 30], "eq_wt4": [2, 30], "equal": [3, 30], "equilibr": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 19, 20, 21, 22, 23, 24, 30, 32], "equlibr": [8, 30], "eras": [16, 29, 34], "error": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "especi": [27, 33], "essenti": [9, 25, 30, 32], "establish": [9, 13, 30], "estim": [9, 12, 30, 31], "et": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "etc": [29, 34], "ethanolamin": 13, "eukaryot": 13, "evalu": [9, 30], "even": 16, "event": [16, 29, 34], "eventu": [1, 2, 3, 7, 16, 18, 30, 32], "everi": [29, 34], "evid": 16, "ewald": [2, 5, 8, 9, 16, 30], "exact": [12, 31], "examin": [9, 30], "exampl": [1, 2, 3, 4, 5, 8, 9, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "example_3jci": [9, 30], "excess": [7, 30], "excit": [13, 16, 17], "exclus": 16, "execut": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 16, 17, 27, 28, 29, 30, 31, 33, 34], "exequiel": 15, "exhibit": [29, 34], "exit": [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 29, 30, 33, 34], "exonucleas": [12, 29, 31, 34], "expand": [13, 35], "expect": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 20, 21, 22, 23, 24, 27, 30, 32, 33], "experi": 16, "experiment": [5, 8, 9, 11, 16, 20, 27, 30, 32, 33], "explain": [29, 34], "explicit": [2, 5, 6, 7, 8, 9, 11, 14, 18, 20, 21, 22, 23, 27], "explicitli": [5, 8, 9, 16, 27, 30, 33], "explor": [13, 14, 16, 17], "explos": [7, 16, 30], "expon": [27, 33], "export": [12, 27, 31, 33], "expr": [12, 31], "extend": [16, 24, 27, 29, 32, 33, 34], "extendedsystem": [27, 33], "extens": [11, 12, 13, 17, 19, 24, 29, 31, 32, 34], "extent": [12, 16, 31], "extern": [12, 24, 31, 32], "extra": [9, 16, 30], "extract": [29, 34], "extrem": [4, 21, 29, 30, 32, 34], "ezequiel": 15, "f": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "facilit": [11, 12, 13, 31, 35], "fact": [29, 34], "factor": [16, 26, 27, 33], "fail": [9, 16, 29, 30, 34], "familiar": [1, 6, 9, 10, 12, 24, 25, 28, 30, 31, 32, 33], "fantast": [9, 30], "faq": [6, 7, 22, 23, 24, 30, 32], "far": [5, 8, 9, 16, 27, 30, 33], "farthest": 16, "fast": 16, "fat": [13, 14, 16], "fc": [20, 23, 24, 32], "fcx": [24, 32], "fcy": [24, 32], "fcz": [24, 32], "feasibl": 13, "featur": [5, 9, 11, 12, 13, 16, 20, 23, 24, 27, 29, 30, 31, 32, 33, 34, 35], "feb": 17, "feel": 17, "fernando": 15, "ferreira": [14, 15], "few": [1, 2, 4, 6, 7, 12, 16, 18, 21, 22, 29, 30, 31, 32, 34], "ff": [9, 12, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 34], "ff0000": [29, 34], "ff10": [3, 30], "ff12sb": [3, 30], "ff14sb": [3, 9, 16, 29, 30, 34], "ff99bsc0": [3, 30], "ffout": [9, 30], "fiber": [19, 32], "field": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35], "fifth": [9, 30], "fight": 17, "figur": [3, 7, 9, 12, 13, 23, 24, 29, 30, 31, 32, 34], "file": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 16, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 31, 34], "filenam": [9, 29, 30, 34], "fill": 16, "final": [9, 19, 24, 27, 29, 30, 32, 33, 34], "find": [1, 2, 3, 4, 6, 7, 9, 12, 22, 23, 24, 29, 30, 31, 32, 34], "fine": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 20, 21, 22, 23, 24, 27, 30, 32, 33], "finish": [12, 29, 31, 34], 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"asp320": 16, "aspart": [5, 8, 9, 16, 20, 27, 30, 32, 33], "aspect": [12, 31], "assembl": [9, 13, 30], "assembli": 17, "assembly1": [9, 30], "assess": [12, 17, 31], "assign": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "associ": 13, "astrid": 15, "asymetr": [9, 30], "asymmetr": [9, 16, 30], "ataxia": 17, "atom": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34, 35], "atomist": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35], "atomselect": [12, 24, 27, 31, 32, 33], "atpas": 17, "attempt": [9, 30], "attent": [5, 8, 9, 20, 27, 30, 32, 33], "auto": [25, 32], "autoimag": [2, 5, 6, 7, 8, 30], "autoinhibit": 17, "automat": [9, 16, 18, 19, 20, 21, 22, 23, 24, 30, 32], "avail": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34], "averag": [12, 29, 31, 34], "avoid": [1, 2, 3, 6, 7, 16, 18, 22, 23, 29, 30, 32, 34], "avx": [12, 29, 31, 34], "avx2": [12, 29, 31, 34], "aw3": [4, 30], "aw5": [4, 21, 30, 32], "awai": [5, 8, 9, 16, 27, 30, 33], "awar": [5, 8, 9, 16, 19, 20, 23, 24, 27, 29, 30, 32, 33, 34], "awk": [9, 30], "axi": [6, 16, 22, 24, 29, 30, 32, 34], "b": [3, 4, 12, 17, 21, 27, 29, 30, 31, 32, 33, 34], "baaden": 17, "back": [5, 8, 9, 16, 18, 20, 21, 22, 23, 24, 27, 30, 32, 33], "backbon": [5, 7, 8, 9, 12, 13, 16, 20, 23, 24, 29, 30, 31, 32, 34], "backmap": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "backmap_less_min": [29, 34], "bad": [6, 7, 16, 22, 30, 32], "balanc": [9, 30], "ballestero": [13, 14, 15, 17], "bar": [27, 33], "barostat": [27, 33], "barrera": [6, 7, 13, 14, 15, 17, 22, 23, 30, 32], "base": [0, 1, 2, 3, 6, 7, 9, 10, 12, 13, 16, 18, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34], "bash": [28, 33], "basi": [17, 29, 34], "basic": [1, 2, 3, 4, 5, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34], "bb": [27, 33], "bb_restraint": [27, 33], "bba": 17, "bc1": [22, 32], "bc13": [7, 30], "bc2": [22, 32], "bc23": [7, 30], "bct": [22, 32], "bct1": [7, 30], "bct2": [7, 30], "bead": [6, 8, 9, 12, 13, 16, 20, 22, 23, 24, 29, 30, 31, 32, 34], "beadi": [8, 30], "beadj": [8, 30], "becam": 16, "becaus": [16, 27, 33], "becom": 16, "been": [9, 11, 13, 16, 18, 19, 20, 21, 22, 30, 32], "befor": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "begin": 16, "behavior": [1, 2, 3, 16, 29, 30, 34], "behind": [16, 24, 32], "being": [16, 35], "bellow": [7, 23, 27, 30, 32, 33], "below": [9, 12, 29, 30, 31, 34], "bend": [13, 17], "benefici": [11, 14], "berger": [0, 30], "bertipaglia": 17, "besid": [29, 34], "best": [2, 5, 6, 7, 8, 9, 20, 23, 24, 27, 29, 30, 32, 33, 34], "beta": [27, 29, 33, 34], "between": [6, 7, 9, 12, 13, 16, 18, 22, 23, 24, 29, 30, 31, 32, 34], "beyond": [7, 30], "bfo": [6, 22, 23, 30, 32], "big": [12, 16, 31], "bigger": 16, "bilay": 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31, 32, 33, 34], "box_xi": [22, 32], "brandner": [14, 15, 17], "brazilian": 17, "break": 16, "breath": [13, 17], "bridg": [5, 9, 27, 30, 33], "brief": 17, "bring": [27, 33], "brini": 17, "bruno": [13, 17], "bsb": 17, "bsc0": [3, 30], "bsc1": [3, 30], "bsg": [5, 8, 9, 16, 27, 30, 33], "bt": [18, 19, 20, 21, 24, 32], "bubbl": [13, 16, 17], "buffer": [3, 30], "bug": [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "build": [10, 16, 25, 28], "built": [12, 29, 31, 34], "bulk": [17, 19, 24, 32], "bulkier": 13, "buratto": [13, 17], "button": [12, 29, 31, 34], "byfram": [29, 34], "byre": [29, 34], "c": [1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 34], "c1": 13, "c1x": [4, 30], "c5": 13, "c5x": [12, 29, 31, 34], "ca": [9, 30], "ca2": 17, "caballero": [13, 14], "calc_n": [9, 30], "calcium": 13, "calcul": [6, 12, 16, 22, 27, 29, 31, 32, 33, 34], "call": [1, 2, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "calmodulin": 17, "cal\u00ec": 17, "can": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "cantero": [27, 33], "cap": [1, 2, 3, 18, 30, 32], "capabl": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33, 35], "capsid": [9, 13, 30], "capsom": [9, 30], "captur": 11, "carafoli": 17, "carbon": [12, 13, 31], "card": [27, 33], "care": [16, 26], "carefulli": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "carlo": 15, "carrasco": [13, 14], "carrer": [13, 17], "carri": [16, 18, 20, 21, 22, 23, 24, 27, 32, 33], "casalla": [13, 14, 17], "case": [5, 7, 8, 9, 10, 12, 16, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34], "caspas": 17, "castro": 17, "cat": [5, 8, 9, 27, 30, 33], "catalysi": 16, "catalyst": 16, "cation": 14, "caus": 16, "caution": [6, 7, 16, 22, 23, 24, 30, 32], "caviti": 16, "cax": [29, 34], "ccdna": [4, 21, 30, 32], "ccdna_cg": [4, 21, 30, 32], "ccdna_cg_box": [21, 32], "ccdna_cg_em": [4, 21, 30, 32], "ccdna_cg_eq": [4, 21, 30, 32], "ccdna_cg_ion": [21, 32], "ccdna_cg_md": [4, 21, 30, 32], "ccdna_cg_md_pbc": [21, 32], "ccdna_cg_sol": [21, 32], "cd": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 30, 32, 33], "cdot": [0, 30], "celiac": 17, "cell": [27, 33], "cellbasisvector": [27, 33], "cellbasisvector1": [27, 33], "cellbasisvector2": [27, 33], "cellbasisvector3": [27, 33], "cellorigin": [27, 33], "cellular": 13, "center": [7, 9, 12, 16, 18, 19, 20, 21, 24, 30, 31, 32], "certain": [11, 18, 19, 20, 21, 22, 29, 32, 34], "certainli": 16, "cg": [11, 12, 13, 14, 16, 17, 19, 31, 35], "cgconv": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 20, 21, 22, 23, 24, 27, 29, 30, 32, 33, 34], "chain": [5, 7, 8, 9, 11, 13, 16, 18, 20, 23, 24, 27, 30, 32, 33, 35], "challeng": 11, "chang": [9, 10, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34], "channel": 13, "chapter": [6, 22, 30, 32], "characterist": [6, 7, 13, 30], "charg": [2, 5, 7, 8, 13, 16, 20, 23, 24, 27, 29, 32, 33, 34], "charmm": [0, 5, 7, 8, 9, 16, 19, 20, 23, 24, 26, 27, 30, 32, 33], "charmm_lipid": [0, 30], "check": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "chemic": [11, 13, 14, 17, 35], "chemistri": [17, 29, 34], "chirdo": 17, "chlorid": 13, "chngmask": [2, 5, 8, 9, 16, 30], "choic": [19, 32], "cholin": 13, "choos": [5, 7, 8, 9, 12, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "chose": [29, 34], "chosen": [19, 32], "cif": [9, 30], "circl": [21, 32], "circoviru": [9, 30], "circular": [4, 21], "circumv": [9, 30], "cite": [11, 14], "citiu": [13, 14], "ckp": [0, 30], "cl": [2, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "clash": [7, 9, 16, 30], "classic": 13, "classif": [29, 34], "classifi": [29, 34], "clean": [27, 29, 33, 34], "click": [7, 9, 12, 23, 29, 30, 31, 32, 34], "clip": [7, 23, 30, 32], "close": [2, 4, 5, 6, 8, 9, 12, 16, 19, 21, 27, 29, 31, 33, 34], "cluster": 16, "clw": [2, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 32, 33, 34], "cmm": [22, 23, 32], "coars": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34, 35], "code": [5, 6, 7, 8, 9, 11, 16, 23, 24, 26, 27, 29, 30, 32, 33, 34, 35], "coeffici": [27, 33], "cof": 11, "cohes": [7, 30], "coil": [16, 29, 34], "coincident": 16, "collaps": 16, "collect": [11, 13, 35], "color": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "column": [27, 33], "combin": [11, 16, 19, 29, 32, 34, 35], "come": [24, 32], "command": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "commandnam": [29, 34], "comment": [27, 33], "common": [9, 11, 12, 16, 26, 30, 31], "commonli": [1, 2, 3, 4, 5, 6, 7, 8, 9, 30], "commun": [11, 17, 35], "compact": [12, 18, 19, 20, 21, 24, 31, 32], "compar": [11, 12, 31, 35], "comparison": 26, "compart": [9, 30], "compat": [0, 5, 8, 9, 11, 12, 13, 16, 20, 23, 24, 27, 30, 31, 32, 33], "compens": [9, 30], "compil": [29, 34], "complain": [23, 24, 32], "complementar": 13, "complet": [7, 9, 12, 13, 23, 24, 30, 31, 32], "complex": [9, 11, 12, 13, 14, 17, 29, 30, 31, 34, 35], "compli": [9, 30], "compon": [12, 13, 29, 31, 34, 35], "compos": [1, 2, 3, 4, 6, 18, 21, 22, 30, 32], "compound": [18, 19, 20, 21, 22, 23, 24, 32], "comprehens": [9, 13, 30], "compromis": 16, "comput": [9, 10, 11, 12, 13, 14, 16, 17, 25, 28, 30, 31, 32, 33], "concaten": [7, 23, 30, 32], "concentr": [2, 5, 6, 7, 8, 9, 12, 18, 19, 20, 21, 22, 23, 24, 27, 31, 32, 33], "concern": 16, "conda": [9, 29, 30, 34], "condit": [2, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 34], "conduct": [9, 12, 13, 30, 31], "conf": [27, 33], "configur": [6, 13, 22, 27, 30, 32, 33], "conflict": [0, 16, 30], "conform": [11, 12, 16, 17, 24, 29, 31, 32, 34], "conjug": [29, 34], "conjunct": [12, 31], "connect": 16, "connexin": 13, "consecut": [29, 34], "consequ": [16, 29, 34], "consexp": [27, 33], "consid": [3, 6, 7, 9, 13, 16, 22, 30, 32], "consider": [29, 34], "consist": [11, 13, 16, 29, 34, 35], "conskcol": [27, 33], "conskfil": [27, 33], "consol": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "consref": [27, 33], "constant": [26, 27, 33], "constantli": 35, "constitut": 16, "constraint": [27, 33], "constraintsc": [27, 33], "construct": [9, 29, 30, 34, 35], "consult": [22, 23, 24, 32], "consum": [3, 6, 7, 30], "contact": [6, 12, 16, 19, 22, 31], "contain": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34], "context": 16, "contextu": [3, 30], "continu": 16, "contrari": 16, "contrast": [12, 27, 31, 33], "control": [27, 29, 33, 34], "conveni": [12, 18, 31, 32], "convent": [0, 6, 7, 16, 22, 23, 30, 32], "converg": [11, 29, 34], "convers": 26, "convert": [0, 8, 16, 18, 19, 20, 21, 22, 23, 24, 26, 29, 30, 32, 34], "coor": [27, 33], "coordin": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 23, 24, 27, 29, 30, 31, 32, 33, 34], "copi": [24, 27, 32, 33], "core": [9, 16, 27, 30, 33], "correct": [5, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30, 31, 32, 33, 34], "correctli": [9, 16, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 34], "correl": [27, 33], "correspond": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 30, 31, 32, 33], "cost": 13, "could": [16, 24, 29, 32, 34], "coulomb": 26, "count": [9, 30], "countcharg": [9, 30], "counterion": [2, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "coupl": [16, 29, 34], "cours": [1, 2, 3, 9, 30], "cov": 17, "coval": [4, 11, 13, 30, 35], "cover": [13, 29, 34], "cp": [18, 19, 20, 21, 22, 23, 24, 27, 32, 33], "cpk": [29, 34], "cpptraj": [2, 5, 8, 9, 16], "cpu": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 27, 29, 30, 31, 32, 33, 34], "crash": 16, "crate": [23, 32], "crd": 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14, 15, 17, 18, 19, 20, 21, 29, 30, 32, 34], "d1": 16, "d2": 16, "d6": 16, "dalk": [12, 29, 31, 34], "damag": 17, "damiano": 17, "damp": [27, 33], "dan": [1, 2, 4, 13, 14, 15, 16, 17, 18, 20, 21, 30, 32], "daniela": 15, "dark": [29, 34], "darkviolet": [29, 34], "darr\u00e9": [5, 8, 9, 13, 14, 15, 17, 18, 19, 20, 24, 27, 30, 32, 33], "dat": [6, 9, 10, 12, 16, 21, 23, 25, 28, 30, 31, 32, 33], "data": [9, 11, 12, 17, 29, 30, 31, 34], "databas": [7, 11, 16, 23, 30, 32], "dataset": 17, "dcd": [27, 33], "dcx": [4, 21, 30, 32], "de": [11, 17, 29, 34], "dec": [29, 34], "decai": [27, 33], "decomposit": [29, 34], "decompress": [9, 30], "dedic": [12, 31], "default": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "defect": 16, "deffnm": [18, 19, 20, 21, 22, 23, 24, 32], "defin": [5, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 26, 27, 29, 30, 31, 32, 33, 34], "definit": [1, 2, 3, 5, 8, 9, 10, 16, 19, 25, 28, 30, 32, 33], "deform": [16, 29, 34], "degre": 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12, 13, 14, 16, 17, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "dz": [27, 33], "e": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "each": [2, 3, 5, 6, 7, 8, 9, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "easili": 16, "echo": [2, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 30, 32], "edg": [13, 27, 33], "edit": [9, 18, 19, 20, 21, 22, 23, 24, 26, 29, 30, 32, 34], "editconf": [18, 19, 20, 21, 22, 23, 24, 32], "editor": [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 27, 30, 32, 33], "edr": [22, 32], "edu": [12, 29, 31, 34], "effect": [1, 2, 3, 13, 16, 18, 30, 32], "effici": [11, 35], "either": 16, "elast": 16, "electr": [13, 16, 17], "electrolyt": [2, 5, 6, 7, 8, 9, 13, 14, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "electropor": 16, "electrostat": [13, 14, 26, 29, 34], "element": [16, 29, 34], "elsewher": [29, 34], "em": [16, 18, 19, 21, 22, 32], "em1": [20, 23, 24, 27, 32, 33], "em1_cgliprot": [23, 32], "em1_cgprot": [20, 24, 32], "em1_prot": [7, 30], "em1_wt4": [5, 8, 30], "em2": [20, 23, 24, 27, 32, 33], "em2_cgliprot": [23, 32], "em2_cgprot": [20, 24, 32], "em2_prot": [7, 30], "em2_wt4": [5, 8, 30], "em3": [24, 32], "em3_cgprot": [24, 32], "em_cgdna": [18, 21, 32], "em_cglip": [22, 32], "em_cpu": [9, 30], "em_gb": [1, 30], "em_gbsa": [4, 30], "em_hyb": [3, 30], "em_hybsol": [19, 32], "em_lipid": [6, 30], "em_wt4": [2, 30], "email": [12, 29, 31, 34], "embed": [2, 7, 19, 23, 24, 30, 32], "embrac": [5, 30], "empir": 16, "emploi": [9, 13, 24, 28, 30, 32, 33], "empti": [8, 30], "enabl": [13, 27, 33], "enantioselect": 16, "enclos": [24, 32], "encompass": 11, "encourag": [27, 33], "end": [1, 2, 3, 4, 9, 18, 21, 22, 24, 27, 30, 32, 33], "endif": [18, 20, 23, 24, 32], "energi": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 19, 20, 21, 22, 23, 24, 26, 30, 32], "engin": [13, 16], "enhanc": [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "enough": [16, 24, 32], "ensembl": [11, 16, 35], "ensur": [9, 11, 13, 30, 35], "entail": 13, "enter": [9, 12, 29, 30, 31, 34], "entir": [7, 11, 13, 23, 29, 32, 34, 35], "entri": [29, 34], "enumer": [23, 32], "envelop": 9, "environ": [16, 29, 34], "epsilon": [5, 8, 9, 16, 20, 27, 30, 32, 33], "eq": [18, 19, 21, 22, 32], "eq1": [20, 23, 24, 27, 32, 33], "eq1_cgliprot": [23, 32], "eq1_cgprot": [20, 24, 32], "eq1_wt4": [5, 8, 30], "eq2": [20, 23, 24, 27, 32, 33], "eq2_cgliprot": [23, 32], "eq2_cgprot": [20, 24, 32], "eq2_wt4": [5, 8, 30], "eq_cgdna": [18, 21, 32], "eq_cglip": [22, 32], "eq_gb": [1, 2, 3, 30], "eq_gbsa": [4, 30], "eq_hyb": [3, 30], "eq_hybsol": [19, 32], "eq_lipid": [6, 30], "eq_prot": [7, 30], "eq_wt4": [2, 30], "equal": [3, 30], "equilibr": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 19, 20, 21, 22, 23, 24, 30, 32], "equlibr": [8, 30], "eras": [16, 29, 34], "error": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "especi": [27, 33], "essenti": [9, 25, 30, 32], "establish": [9, 13, 30], "estim": [9, 12, 30, 31], "et": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "etc": [29, 34], "ethanolamin": 13, "eukaryot": 13, "evalu": [9, 30], "even": 16, "event": [16, 29, 34], "eventu": [1, 2, 3, 7, 16, 18, 30, 32], "everi": [29, 34], "evid": 16, "ewald": [2, 5, 8, 9, 16, 30], "exact": [12, 31], "examin": [9, 30], "exampl": [1, 2, 3, 4, 5, 8, 9, 12, 13, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "example_3jci": [9, 30], "excess": [7, 30], "excit": [13, 16, 17], "exclus": 16, "execut": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 16, 17, 27, 28, 29, 30, 31, 33, 34], "exequiel": 15, "exhibit": [29, 34], "exit": [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 29, 30, 33, 34], "exonucleas": [12, 29, 31, 34], "expand": [13, 35], "expect": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 20, 21, 22, 23, 24, 27, 30, 32, 33], "experi": 16, "experiment": [5, 8, 9, 11, 16, 20, 27, 30, 32, 33], 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"feasibl": 13, "featur": [5, 9, 11, 12, 13, 16, 20, 23, 24, 27, 29, 30, 31, 32, 33, 34, 35], "feb": 17, "feel": 17, "fernando": 15, "ferreira": [14, 15], "few": [1, 2, 4, 6, 7, 12, 16, 18, 21, 22, 29, 30, 31, 32, 34], "ff": [9, 12, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 34], "ff0000": [29, 34], "ff10": [3, 30], "ff12sb": [3, 30], "ff14sb": [3, 9, 16, 29, 30, 34], "ff99bsc0": [3, 30], "ffout": [9, 30], "fiber": [19, 32], "field": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35], "fifth": [9, 30], "fight": 17, "figur": [3, 7, 9, 12, 13, 23, 24, 29, 30, 31, 32, 34], "file": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 16, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 31, 34], "filenam": [9, 29, 30, 34], "fill": 16, "final": [9, 19, 24, 27, 29, 30, 32, 33, 34], "find": [1, 2, 3, 4, 6, 7, 9, 12, 22, 23, 24, 29, 30, 31, 32, 34], "fine": [1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 18, 20, 21, 22, 23, 24, 27, 30, 32, 33], "finish": [12, 29, 31, 34], "first": [1, 2, 6, 7, 9, 12, 16, 23, 24, 27, 29, 30, 31, 32, 33, 34], "fit": [12, 31], "five": [9, 13, 30], "fix": [6, 7, 9, 16, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "fixpdb": [9, 30], "flag": [1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 18, 19, 20, 21, 22, 23, 24, 27, 29, 30, 31, 32, 33, 34], "flexibl": [13, 17, 27, 29, 33, 34], "florencia": 15, "fluctuat": [6, 7, 12, 16, 30, 31], "fma": [12, 29, 31, 34], "focem": 11, "focu": [12, 13, 14, 29, 31, 34], "focus": 13, "fold": [11, 16], "folder": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 30, 32, 33], "follow": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35], "font": [29, 34], "fontsiz": [29, 34], "forc": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35], "forcefield": [19, 32], "forg": [9, 30], "forget": [18, 19, 20, 21, 22, 23, 24, 32], "form": [3, 5, 9, 12, 13, 16, 17, 20, 23, 24, 27, 30, 31, 32, 33], "format": [1, 2, 3, 7, 8, 9, 11, 13, 16, 27, 30, 33], "former": [16, 27, 33], "fortiu": [13, 14], "found": [1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 16, 18, 19, 20, 21, 22, 23, 24, 27, 30, 32, 33], "foundat": 11, "four": [13, 14, 29, 34], "fourth": [9, 30], "frac": [0, 6, 22, 30, 32], "fragment": [0, 6, 7, 9, 12, 16, 22, 23, 29, 30, 31, 32, 34], "frai": [1, 2, 3, 18, 30, 32], "frame": [12, 29, 31, 34], "framework": [13, 16], "frankensteinian": 16, "free": [11, 12, 16, 17, 29, 31, 34], "freedom": 16, "freeli": [10, 25, 28, 30, 32, 33], "frequent": [7, 13, 16, 30], "frigini": [13, 14, 15, 17], "frizzarin": 17, "from": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34], "frontier": [13, 17], "fulli": 13, "funct": [24, 32], "function": [9, 13, 27, 28, 29, 30, 33, 34], "fund": 11, "further": [14, 24, 32, 35], "furthermor": [29, 34], "g": [0, 2, 5, 6, 7, 8, 9, 13, 14, 16, 17, 18, 19, 20, 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