diff --git a/input/lysozyme/lys_Gd_salt_solvated.mol b/input/lysozyme/lys_Gd_salt_solvated.mol new file mode 100755 index 0000000..0f802b0 --- /dev/null +++ b/input/lysozyme/lys_Gd_salt_solvated.mol @@ -0,0 +1,97 @@ +#ATOMS +C 615.16 +N 195.16 +O 887.2 +Na 19.44 +S 10 +Cl 18.36 +Gd_fast 3.08 + +#VOLUME +30820 // Volume per molecule in Angstrom^3. +500 // Length scale of sample in Angstrom. Used for effective escape rate of photo-electrons (assumes surrounded by a void). +none // Spatial boundary shape - options are none, spherical, cylindrical, planar + +#PULSE +7112 // Photon energy in eV. +15 // Pulse width in femtoseconds (defined as FWHM for Gaussian pulse). +gaussian // Pulse shape + +#USE_COUNT +true // active (using count)? +1.75 // Photon density (x10^12 ph.µm-2) (3.5e12 um-2) + +#NUMERICAL +2000 // Initial guess for number of time step points for rate equation. +24 // Number of threads in OpenMP. + +#DYNAMIC_GRID +M // Grid regions preset, options are: dismal, low, medium, high, (referring to accuracy), and no_dirac (static region is used rather than dynamic dirac regions) +5.05 // Grid update period in fs, (dynamic grid only). +2 // Time before transforming initial guess grid to dynamic grid in fs. + +#OUTPUT +800 // Number of time steps in the output files. +4000 // number of free-electron grid points in output file. +N // Write atomic charges in a separate file (Y/N)? +Y // Write intensity in a separate file (Y/N)? +Y // Write data for molecular dynamics (MD) in a separate file (Y/N)? + +#DEBUG +99 //10 // Simulation cutoff time in fs +0.01 // Interval to update current timestep [fs]. +0 // Interval **in steps** between live plot (_live_plot.png) updates +120 // Period between backups in minutes +####END##### + +Notes: + +Hen egg-white lysozyme https://files.rcsb.org/pub/pdb/validation_reports/et/4et8/4et8_full_validation.pdf +gadolinium included + +Using solvent parameters of Nass et al 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7156470/ : + +Storage solution: + +10% NaCl, 0.1 M Na acetate pH 4.0 + +Slurry supplemented with: +0.1 M gadoteridol + +-> 1.71 M NaCl ++ 0.1 M Na ++ 0.2 M C ++ 0.2 M O ++ 0.3 M H ( ignored ) ++ 0.1 M Gd + +-> additional 18 Na, 17 Cl, 2 C, 2 O for every solvated Gd. + + + + + +Protein: + +C 613 +N 193 +O 185 +S 10 +Gd_fast 2 + +volume 20k +---- + +Solvated - solvent content is 35.11 based on 6sr5, and noting that Gd density is basically same in solution and protein, get Gd + 1.08. +Molarity of water, assume about 50 M (1 Gd for every 500 O): + + +C 615.16 +N 195.16 +O 887.2 +Na 19.44 +Cl 18.36 +S 10 +Gd_fast 3.08 + +volume 30.82k diff --git a/input/lysozyme/lys_Gd_salt_solvated_fast.mol b/input/lysozyme/lys_Gd_salt_solvated_fast.mol new file mode 100755 index 0000000..b6bcb08 --- /dev/null +++ b/input/lysozyme/lys_Gd_salt_solvated_fast.mol @@ -0,0 +1,103 @@ +#ATOMS +C 615.16 +N 195.16 +O 887.2 +Na 19.44 +S 10 +Cl 18.36 +Gd_fast 3.08 + +#BOUND_FREE_EXCLUSIONS +Gd_fast +Na +S +Cl + +#VOLUME +30820 // Volume per molecule in Angstrom^3. +500 // Length scale of sample in Angstrom. Used for effective escape rate of photo-electrons (assumes surrounded by a void). +none // Spatial boundary shape - options are none, spherical, cylindrical, planar + +#PULSE +7112 // Photon energy in eV. +15 // Pulse width in femtoseconds (defined as FWHM for Gaussian pulse). +gaussian // Pulse shape + +#USE_COUNT +true // active (using count)? +1.75 // Photon density (x10^12 ph.µm-2) (3.5e12 um-2) + +#NUMERICAL +2000 // Initial guess for number of time step points for rate equation. +24 // Number of threads in OpenMP. + +#DYNAMIC_GRID +M // Grid regions preset, options are: dismal, low, medium, high, (referring to accuracy), and no_dirac (static region is used rather than dynamic dirac regions) +5.05 // Grid update period in fs, (dynamic grid only). +2 // Time before transforming initial guess grid to dynamic grid in fs. + +#OUTPUT +800 // Number of time steps in the output files. +4000 // number of free-electron grid points in output file. +N // Write atomic charges in a separate file (Y/N)? +Y // Write intensity in a separate file (Y/N)? +Y // Write data for molecular dynamics (MD) in a separate file (Y/N)? + +#DEBUG +99 //10 // Simulation cutoff time in fs +0.01 // Interval to update current timestep [fs]. +0 // Interval **in steps** between live plot (_live_plot.png) updates +90 // Period between backups in minutes +####END##### + +Notes: + +Hen egg-white lysozyme https://files.rcsb.org/pub/pdb/validation_reports/et/4et8/4et8_full_validation.pdf +gadolinium included + +Using solvent parameters of Nass et al 2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7156470/ : + +Storage solution: + +10% NaCl, 0.1 M Na acetate pH 4.0 + +Slurry supplemented with: +0.1 M gadoteridol + +-> 1.71 M NaCl ++ 0.1 M Na ++ 0.2 M C ++ 0.2 M O ++ 0.3 M H ( ignored ) ++ 0.1 M Gd + +-> additional 18 Na, 17 Cl, 2 C, 2 O for every solvated Gd. + + + + + +Protein: + +C 613 +N 193 +O 185 +S 10 +Gd_fast 2 + +volume 20k +---- + +Solvated - solvent content is 35.11 based on 6sr5, and noting that Gd density is basically same in solution and protein, get Gd + 1.08. +Molarity of water, assume about 50 M (1 Gd for every 500 O): + + +C 615.16 +N 195.16 +O 887.2 +Na 19.44 +Cl 18.36 +S 10 +Gd_fast 3.08 + +volume 30.82k diff --git a/input/lysozyme/lys_Gd_solvated.mol b/input/lysozyme/lys_Gd_solvated.mol new file mode 100755 index 0000000..4972b30 --- /dev/null +++ b/input/lysozyme/lys_Gd_solvated.mol @@ -0,0 +1,52 @@ +#ATOMS +C 615.16 +N 195.16 +O 887.2 +S 10 +Gd_fast 3.08 + + + +#VOLUME +30820 // Volume per molecule in Angstrom^3. +500 // Length scale of sample in Angstrom. Used for effective escape rate of photo-electrons (assumes surrounded by a void). +none // Spatial boundary shape - options are none, spherical, cylindrical, planar + + +#PULSE +7112 // Photon energy in eV. +15 // Pulse width in femtoseconds (defined as FWHM for Gaussian pulse). +gaussian // Pulse shape + +#USE_COUNT +true // active (using count)? +1.75 // Photon density (x10^12 ph.µm-2) (3.5e12 um-2) + +#NUMERICAL +2000 // Initial guess for number of time step points for rate equation. +24 // Number of threads in OpenMP. + +#DYNAMIC_GRID +M // Grid regions preset, options are: dismal, low, medium, high, (referring to accuracy), and no_dirac (static region is used rather than dynamic dirac regions) +5.05 // Grid update period in fs, (dynamic grid only). +2 // Time before transforming initial guess grid to dynamic grid in fs. + +#OUTPUT +800 // Number of time steps in the output files. +4000 // number of free-electron grid points in output file. +N // Write atomic charges in a separate file (Y/N)? +Y // Write intensity in a separate file (Y/N)? +Y // Write data for molecular dynamics (MD) in a separate file (Y/N)? + +#DEBUG +99 //10 // Simulation cutoff time in fs +0.01 // Interval to update current timestep [fs]. +0 // Interval **in steps** between live plot (_live_plot.png) updates +90 // Period between backups in minutes +####END##### + +Notes: + +see lys_Gd_salt_solvated + +ignoring volume change from removing salt (removing salt probably increases the volume negligibly) \ No newline at end of file diff --git a/input/lysozyme/lys_Gd_solvated_fast.mol b/input/lysozyme/lys_Gd_solvated_fast.mol new file mode 100755 index 0000000..77ff008 --- /dev/null +++ b/input/lysozyme/lys_Gd_solvated_fast.mol @@ -0,0 +1,55 @@ +#ATOMS +C 615.16 +N 195.16 +O 887.2 +S 10 +Gd_fast 3.08 + +#BOUND_FREE_EXCLUSIONS +S +Gd_fast + + +#VOLUME +30820 // Volume per molecule in Angstrom^3. +500 // Length scale of sample in Angstrom. Used for effective escape rate of photo-electrons (assumes surrounded by a void). +none // Spatial boundary shape - options are none, spherical, cylindrical, planar + + +#PULSE +7112 // Photon energy in eV. +15 // Pulse width in femtoseconds (defined as FWHM for Gaussian pulse). +gaussian // Pulse shape + +#USE_COUNT +true // active (using count)? +1.75 // Photon density (x10^12 ph.µm-2) (3.5e12 um-2) + +#NUMERICAL +2000 // Initial guess for number of time step points for rate equation. +24 // Number of threads in OpenMP. + +#DYNAMIC_GRID +M // Grid regions preset, options are: dismal, low, medium, high, (referring to accuracy), and no_dirac (static region is used rather than dynamic dirac regions) +5.05 // Grid update period in fs, (dynamic grid only). +2 // Time before transforming initial guess grid to dynamic grid in fs. + +#OUTPUT +800 // Number of time steps in the output files. +4000 // number of free-electron grid points in output file. +N // Write atomic charges in a separate file (Y/N)? +Y // Write intensity in a separate file (Y/N)? +Y // Write data for molecular dynamics (MD) in a separate file (Y/N)? + +#DEBUG +99 //10 // Simulation cutoff time in fs +0.01 // Interval to update current timestep [fs]. +0 // Interval **in steps** between live plot (_live_plot.png) updates +90 // Period between backups in minutes +####END##### + +Notes: + +see lys_Gd_salt_solvated + +ignoring volume change from removing salt (removing salt probably increases the volume negligibly) \ No newline at end of file diff --git a/input/lysozyme/lys_salt_solvated.mol b/input/lysozyme/lys_salt_solvated.mol new file mode 100755 index 0000000..e0bbfca --- /dev/null +++ b/input/lysozyme/lys_salt_solvated.mol @@ -0,0 +1,50 @@ +#ATOMS +C 615.16 +N 195.16 +O 890.08 +Na 19.44 +S 10 +Cl 18.36 + + + +#VOLUME +30820 // Volume per molecule in Angstrom^3. +500 // Length scale of sample in Angstrom. Used for effective escape rate of photo-electrons (assumes surrounded by a void). +none // Spatial boundary shape - options are none, spherical, cylindrical, planar + + +#PULSE +7112 // Photon energy in eV. +15 // Pulse width in femtoseconds (defined as FWHM for Gaussian pulse). +gaussian // Pulse shape + +#USE_COUNT +true // active (using count)? +1.75 // Photon density (x10^12 ph.µm-2) (3.5e12 um-2) + +#NUMERICAL +2000 // Initial guess for number of time step points for rate equation. +24 // Number of threads in OpenMP. + +#DYNAMIC_GRID +M // Grid regions preset, options are: dismal, low, medium, high, (referring to accuracy), and no_dirac (static region is used rather than dynamic dirac regions) +5.05 // Grid update period in fs, (dynamic grid only). +2 // Time before transforming initial guess grid to dynamic grid in fs. + +#OUTPUT +800 // Number of time steps in the output files. +4000 // number of free-electron grid points in output file. +N // Write atomic charges in a separate file (Y/N)? +Y // Write intensity in a separate file (Y/N)? +Y // Write data for molecular dynamics (MD) in a separate file (Y/N)? + +#DEBUG +99 //10 // Simulation cutoff time in fs +0.01 // Interval to update current timestep [fs]. +####END##### + +Notes: +see lys_gd_solvated + +Gd replaced with waters \ No newline at end of file diff --git a/input/lysozyme/lys_salt_solvated_fast.mol b/input/lysozyme/lys_salt_solvated_fast.mol new file mode 100755 index 0000000..1e40956 --- /dev/null +++ b/input/lysozyme/lys_salt_solvated_fast.mol @@ -0,0 +1,54 @@ +#ATOMS +C 615.16 +N 195.16 +O 890.08 +Na 19.44 +S 10 +Cl 18.36 + +#BOUND_FREE_EXCLUSIONS +S +Na +Cl + + +#VOLUME +30820 // Volume per molecule in Angstrom^3. +500 // Length scale of sample in Angstrom. Used for effective escape rate of photo-electrons (assumes surrounded by a void). +none // Spatial boundary shape - options are none, spherical, cylindrical, planar + + +#PULSE +7112 // Photon energy in eV. +15 // Pulse width in femtoseconds (defined as FWHM for Gaussian pulse). +gaussian // Pulse shape + +#USE_COUNT +true // active (using count)? +1.75 // Photon density (x10^12 ph.µm-2) (3.5e12 um-2) + +#NUMERICAL +2000 // Initial guess for number of time step points for rate equation. +24 // Number of threads in OpenMP. + +#DYNAMIC_GRID +M // Grid regions preset, options are: dismal, low, medium, high, (referring to accuracy), and no_dirac (static region is used rather than dynamic dirac regions) +5.05 // Grid update period in fs, (dynamic grid only). +2 // Time before transforming initial guess grid to dynamic grid in fs. + +#OUTPUT +800 // Number of time steps in the output files. +4000 // number of free-electron grid points in output file. +N // Write atomic charges in a separate file (Y/N)? +Y // Write intensity in a separate file (Y/N)? +Y // Write data for molecular dynamics (MD) in a separate file (Y/N)? + +#DEBUG +99 //10 // Simulation cutoff time in fs +0.01 // Interval to update current timestep [fs]. +####END##### + +Notes: +see lys_gd_solvated + +Gd replaced with waters \ No newline at end of file diff --git a/input/lysozyme/lys_solvated.mol b/input/lysozyme/lys_solvated.mol new file mode 100755 index 0000000..229a644 --- /dev/null +++ b/input/lysozyme/lys_solvated.mol @@ -0,0 +1,48 @@ +#ATOMS +C 615.16 +N 195.16 +O 890.08 +S 10 + + + +#VOLUME +30820 // Volume per molecule in Angstrom^3. +500 // Length scale of sample in Angstrom. Used for effective escape rate of photo-electrons (assumes surrounded by a void). +none // Spatial boundary shape - options are none, spherical, cylindrical, planar + + +#PULSE +7112 // Photon energy in eV. +15 // Pulse width in femtoseconds (defined as FWHM for Gaussian pulse). +gaussian // Pulse shape + +#USE_COUNT +true // active (using count)? +1.75 // Photon density (x10^12 ph.µm-2) (3.5e12 um-2) + +#NUMERICAL +2000 // Initial guess for number of time step points for rate equation. +24 // Number of threads in OpenMP. + +#DYNAMIC_GRID +M // Grid regions preset, options are: dismal, low, medium, high, (referring to accuracy), and no_dirac (static region is used rather than dynamic dirac regions) +5.05 // Grid update period in fs, (dynamic grid only). +2 // Time before transforming initial guess grid to dynamic grid in fs. + +#OUTPUT +800 // Number of time steps in the output files. +4000 // number of free-electron grid points in output file. +N // Write atomic charges in a separate file (Y/N)? +Y // Write intensity in a separate file (Y/N)? +Y // Write data for molecular dynamics (MD) in a separate file (Y/N)? + +#DEBUG +99 //10 // Simulation cutoff time in fs +0.01 // Interval to update current timestep [fs]. +####END##### + +Notes: +see lys_gd_solvated + +Gd replaced with waters \ No newline at end of file diff --git a/input/lysozyme/lys_solvated_light.mol b/input/lysozyme/lys_solvated_light.mol new file mode 100755 index 0000000..3e2d6a7 --- /dev/null +++ b/input/lysozyme/lys_solvated_light.mol @@ -0,0 +1,45 @@ +#ATOMS +C 615.16 +N 205.16 +O 890.08 + +#VOLUME +30820 // Volume per molecule in Angstrom^3. +500 // Length scale of sample in Angstrom. Used for effective escape rate of photo-electrons (assumes surrounded by a void). +none // Spatial boundary shape - options are none, spherical, cylindrical, planar + + +#PULSE +7112 // Photon energy in eV. +15 // Pulse width in femtoseconds (defined as FWHM for Gaussian pulse). +gaussian // Pulse shape + +#USE_COUNT +true // active (using count)? +1.75 // Photon density (x10^12 ph.µm-2) (3.5e12 um-2) + +#NUMERICAL +2000 // Initial guess for number of time step points for rate equation. +24 // Number of threads in OpenMP. + +#DYNAMIC_GRID +M // Grid regions preset, options are: dismal, low, medium, high, (referring to accuracy), and no_dirac (static region is used rather than dynamic dirac regions) +5.05 // Grid update period in fs, (dynamic grid only). +2 // Time before transforming initial guess grid to dynamic grid in fs. + +#OUTPUT +800 // Number of time steps in the output files. +4000 // number of free-electron grid points in output file. +N // Write atomic charges in a separate file (Y/N)? +Y // Write intensity in a separate file (Y/N)? +Y // Write data for molecular dynamics (MD) in a separate file (Y/N)? + +#DEBUG +99 //10 // Simulation cutoff time in fs +0.01 // Interval to update current timestep [fs]. +####END##### + +Notes: +see lys_solvated + +sulfur replaced with N (note this isn't physical, but is to roughly control for density) \ No newline at end of file