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2025
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| Accesso online: | https://doi.org/10.5281/zenodo.17447408 |
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| author | Kotsis, Konstantinos |
| author_facet | Kotsis, Konstantinos |
| contents | <p dir="ltr">Here's a workflow for applying the CASPT2 method to a bio-nano interface, such as a protein adsorbed on a silver nanoparticle, and simulating MP2 dynamics to obtain dynamical properties of the system:</p> <p dir="ltr">CASPT2 Workflow:</p> <p dir="ltr">1. Prepare the system:</p> <p dir="ltr">* Use a molecular mechanics (MM) or molecular dynamics (MD) simulation to prepare the protein structure and adsorb it on the silver nanoparticle.</p> <p dir="ltr">* You can use software like GROMACS, AMBER, or CHARMM for this step.</p> <p dir="ltr">2. Generate the input files:</p> <p dir="ltr">* Use a quantum chemistry software like MOLCAS, GAUSSIAN, or PSI4 to generate the input files for the CASPT2 calculation.</p> <p dir="ltr">* You'll need to specify the basis set, atomic coordinates, and other calculation parameters.</p> <p dir="ltr">3. Perform the CASPT2 calculation:</p> <p dir="ltr">* Use a quantum chemistry software like MOLCAS, GAUSSIAN, or PSI4 to perform the CASPT2 calculation.</p> <p dir="ltr">* This will involve calculating the multiconfigurational self-consistent field (MCSCF) wavefunction, followed by a second-order perturbation theory (PT2) correction.</p> <p dir="ltr">4. Analyze the results:</p> <p dir="ltr">* Use the output files from the CASPT2 calculation to analyze the electronic structure and properties of the bio-nano interface.</p> <p dir="ltr">* You can use software like MOLCAS, GAUSSIAN, or PSI4 to visualize the molecular orbitals, calculate the electron density, and obtain other properties like the adsorption energy.</p> <p dir="ltr">Some software tools that can be used for the CASPT2 workflow are:</p> <p dir="ltr">* MOLCAS: A quantum chemistry software package that can be used for CASPT2 calculations.</p> <p dir="ltr">* GAUSSIAN: A commercial quantum chemistry software package that can be used for CASPT2 calculations.</p> <p dir="ltr">* PSI4: An open-source quantum chemistry software package that can be used for CASPT2 calculations.</p> <p dir="ltr">MP2 Dynamics Workflow:</p> <p dir="ltr">1. Prepare the system:</p> <p dir="ltr">* Use a molecular mechanics (MM) or molecular dynamics (MD) simulation to prepare the protein structure and adsorb it on the silver nanoparticle.</p> <p dir="ltr">* You can use software like GROMACS, AMBER, or CHARMM for this step.</p> <p dir="ltr">2. Generate the input files:</p> <p dir="ltr">* Use a quantum chemistry software like MOLCAS, GAUSSIAN, or PSI4 to generate the input files for the MP2 calculation.</p> <p dir="ltr">* You'll need to specify the basis set, atomic coordinates, and other calculation parameters.</p> <p dir="ltr">3. Perform the MP2 calculation:</p> <p dir="ltr">* Use a quantum chemistry software like MOLCAS, GAUSSIAN, or PSI4 to perform the MP2 calculation.</p> <p dir="ltr">* This will involve calculating the MP2 energy and wavefunction for the bio-nano interface.</p> <p dir="ltr">4. Simulate the dynamics:</p> <p dir="ltr">* Use a software like GROMACS, AMBER, or CHARMM to simulate the dynamics of the bio-nano interface using the MP2 potential energy surface.</p> <p dir="ltr">* You can use methods like molecular dynamics (MD) or Monte Carlo (MC) simulations to sample the configuration space and obtain dynamical properties like the adsorption energy, diffusion coefficient, and other transport properties.</p> <p dir="ltr">5. Analyze the results:</p> <p dir="ltr">* Use the output files from the dynamics simulation to analyze the dynamical properties of the bio-nano interface.</p> <p dir="ltr">* You can use software like GROMACS, AMBER, or CHARMM to visualize the trajectory, calculate the autocorrelation functions, and obtain other properties like the velocity autocorrelation function.</p> <p dir="ltr">Some software tools that can be used for the MP2 dynamics workflow are:</p> <p dir="ltr">* GROMACS: A molecular dynamics simulation software package that can be used for MP2 dynamics simulations.</p> <p dir="ltr">* AMBER: A molecular dynamics simulation software package that can be used for MP2 dynamics simulations.</p> <p dir="ltr">* CHARMM: A molecular dynamics simulation software package that can be used for MP2 dynamics simulations.</p> <p dir="ltr">* MOLCAS: A quantum chemistry software package that can be used for MP2 calculations.</p> <p dir="ltr">* GAUSSIAN: A commercial quantum chemistry software package that can be used for MP2 calculations.</p> <p dir="ltr">* PSI4: An open-source quantum chemistry software package that can be used for MP2 calculations.</p> <p dir="ltr">Here is an example of how to use the MOLCAS software to perform a CASPT2 calculation on a protein adsorbed on a silver nanoparticle:</p> <p dir="ltr"># Define the protein and silver nanoparticle structures</p> <p dir="ltr">protein_structure = 'protein.pdb'</p> <p dir="ltr">silver_nanoparticle_structure = 'silver_nanoparticle.xyz'</p> <p dir="ltr"># Define the basis set and calculation parameters</p> <p dir="ltr">basis_set = 'ANO-RCC-VDZP'</p> <p dir="ltr">calculation_parameters = {</p> <p dir="ltr"> 'method': 'CASPT2',</p> <p dir="ltr"> 'num_states': 5,</p> <p dir="ltr"> 'root': 1</p> <p dir="ltr">}</p> <p dir="ltr"># Perform the CASPT2 calculation</p> <p dir="ltr">import molcas</p> <p dir="ltr">calculation = molcas.Caspt2(</p> <p dir="ltr"> molecule=protein_structure,</p> <p dir="ltr"> basis_set=basis_set,</p> <p dir="ltr"> parameters=calculation_parameters</p> <p dir="ltr">)</p> <p dir="ltr">calculation.run()</p> <p dir="ltr"># Analyze the results</p> <p dir="ltr">results = calculation.get_results()</p> <p dir="ltr">print(results)</p> <p dir="ltr">And here is an example of how to use the GROMACS software to simulate MP2 dynamics:</p> <p dir="ltr"># Define the protein and silver nanoparticle structures</p> <p dir="ltr">protein_structure = 'protein.gro'</p> <p dir="ltr">silver_nanoparticle_structure = 'silver_nanoparticle.gro'</p> <p dir="ltr"># Define the MP2 potential energy surface</p> <p dir="ltr">mp2_potential = 'mp2.pot'</p> <p dir="ltr"># Simulate the dynamics</p> <p dir="ltr">import gromacs</p> <p dir="ltr">simulation = gromacs.MD(</p> <p dir="ltr"> molecule=protein_structure,</p> <p dir="ltr"> potential=mp2_potential,</p> <p dir="ltr"> integrator='verlet',</p> <p dir="ltr"> dt=0.1,</p> <p dir="ltr"> nsteps=100000</p> <p dir="ltr">)</p> <p dir="ltr">simulation.run()</p> <p dir="ltr"># Analyze the results</p> <p dir="ltr">results = simulation.get_results()</p> <p dir="ltr">print(results)</p> <p dir="ltr">Note that these are highly simplified examples, and in practice, more complex calculations and simulations would be required to obtain accurate results.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17447408 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | CASPT2 and MP2 dynamics of the bionano interface Kotsis, Konstantinos <p dir="ltr">Here's a workflow for applying the CASPT2 method to a bio-nano interface, such as a protein adsorbed on a silver nanoparticle, and simulating MP2 dynamics to obtain dynamical properties of the system:</p> <p dir="ltr">CASPT2 Workflow:</p> <p dir="ltr">1. Prepare the system:</p> <p dir="ltr">* Use a molecular mechanics (MM) or molecular dynamics (MD) simulation to prepare the protein structure and adsorb it on the silver nanoparticle.</p> <p dir="ltr">* You can use software like GROMACS, AMBER, or CHARMM for this step.</p> <p dir="ltr">2. Generate the input files:</p> <p dir="ltr">* Use a quantum chemistry software like MOLCAS, GAUSSIAN, or PSI4 to generate the input files for the CASPT2 calculation.</p> <p dir="ltr">* You'll need to specify the basis set, atomic coordinates, and other calculation parameters.</p> <p dir="ltr">3. Perform the CASPT2 calculation:</p> <p dir="ltr">* Use a quantum chemistry software like MOLCAS, GAUSSIAN, or PSI4 to perform the CASPT2 calculation.</p> <p dir="ltr">* This will involve calculating the multiconfigurational self-consistent field (MCSCF) wavefunction, followed by a second-order perturbation theory (PT2) correction.</p> <p dir="ltr">4. Analyze the results:</p> <p dir="ltr">* Use the output files from the CASPT2 calculation to analyze the electronic structure and properties of the bio-nano interface.</p> <p dir="ltr">* You can use software like MOLCAS, GAUSSIAN, or PSI4 to visualize the molecular orbitals, calculate the electron density, and obtain other properties like the adsorption energy.</p> <p dir="ltr">Some software tools that can be used for the CASPT2 workflow are:</p> <p dir="ltr">* MOLCAS: A quantum chemistry software package that can be used for CASPT2 calculations.</p> <p dir="ltr">* GAUSSIAN: A commercial quantum chemistry software package that can be used for CASPT2 calculations.</p> <p dir="ltr">* PSI4: An open-source quantum chemistry software package that can be used for CASPT2 calculations.</p> <p dir="ltr">MP2 Dynamics Workflow:</p> <p dir="ltr">1. Prepare the system:</p> <p dir="ltr">* Use a molecular mechanics (MM) or molecular dynamics (MD) simulation to prepare the protein structure and adsorb it on the silver nanoparticle.</p> <p dir="ltr">* You can use software like GROMACS, AMBER, or CHARMM for this step.</p> <p dir="ltr">2. Generate the input files:</p> <p dir="ltr">* Use a quantum chemistry software like MOLCAS, GAUSSIAN, or PSI4 to generate the input files for the MP2 calculation.</p> <p dir="ltr">* You'll need to specify the basis set, atomic coordinates, and other calculation parameters.</p> <p dir="ltr">3. Perform the MP2 calculation:</p> <p dir="ltr">* Use a quantum chemistry software like MOLCAS, GAUSSIAN, or PSI4 to perform the MP2 calculation.</p> <p dir="ltr">* This will involve calculating the MP2 energy and wavefunction for the bio-nano interface.</p> <p dir="ltr">4. Simulate the dynamics:</p> <p dir="ltr">* Use a software like GROMACS, AMBER, or CHARMM to simulate the dynamics of the bio-nano interface using the MP2 potential energy surface.</p> <p dir="ltr">* You can use methods like molecular dynamics (MD) or Monte Carlo (MC) simulations to sample the configuration space and obtain dynamical properties like the adsorption energy, diffusion coefficient, and other transport properties.</p> <p dir="ltr">5. Analyze the results:</p> <p dir="ltr">* Use the output files from the dynamics simulation to analyze the dynamical properties of the bio-nano interface.</p> <p dir="ltr">* You can use software like GROMACS, AMBER, or CHARMM to visualize the trajectory, calculate the autocorrelation functions, and obtain other properties like the velocity autocorrelation function.</p> <p dir="ltr">Some software tools that can be used for the MP2 dynamics workflow are:</p> <p dir="ltr">* GROMACS: A molecular dynamics simulation software package that can be used for MP2 dynamics simulations.</p> <p dir="ltr">* AMBER: A molecular dynamics simulation software package that can be used for MP2 dynamics simulations.</p> <p dir="ltr">* CHARMM: A molecular dynamics simulation software package that can be used for MP2 dynamics simulations.</p> <p dir="ltr">* MOLCAS: A quantum chemistry software package that can be used for MP2 calculations.</p> <p dir="ltr">* GAUSSIAN: A commercial quantum chemistry software package that can be used for MP2 calculations.</p> <p dir="ltr">* PSI4: An open-source quantum chemistry software package that can be used for MP2 calculations.</p> <p dir="ltr">Here is an example of how to use the MOLCAS software to perform a CASPT2 calculation on a protein adsorbed on a silver nanoparticle:</p> <p dir="ltr"># Define the protein and silver nanoparticle structures</p> <p dir="ltr">protein_structure = 'protein.pdb'</p> <p dir="ltr">silver_nanoparticle_structure = 'silver_nanoparticle.xyz'</p> <p dir="ltr"># Define the basis set and calculation parameters</p> <p dir="ltr">basis_set = 'ANO-RCC-VDZP'</p> <p dir="ltr">calculation_parameters = {</p> <p dir="ltr"> 'method': 'CASPT2',</p> <p dir="ltr"> 'num_states': 5,</p> <p dir="ltr"> 'root': 1</p> <p dir="ltr">}</p> <p dir="ltr"># Perform the CASPT2 calculation</p> <p dir="ltr">import molcas</p> <p dir="ltr">calculation = molcas.Caspt2(</p> <p dir="ltr"> molecule=protein_structure,</p> <p dir="ltr"> basis_set=basis_set,</p> <p dir="ltr"> parameters=calculation_parameters</p> <p dir="ltr">)</p> <p dir="ltr">calculation.run()</p> <p dir="ltr"># Analyze the results</p> <p dir="ltr">results = calculation.get_results()</p> <p dir="ltr">print(results)</p> <p dir="ltr">And here is an example of how to use the GROMACS software to simulate MP2 dynamics:</p> <p dir="ltr"># Define the protein and silver nanoparticle structures</p> <p dir="ltr">protein_structure = 'protein.gro'</p> <p dir="ltr">silver_nanoparticle_structure = 'silver_nanoparticle.gro'</p> <p dir="ltr"># Define the MP2 potential energy surface</p> <p dir="ltr">mp2_potential = 'mp2.pot'</p> <p dir="ltr"># Simulate the dynamics</p> <p dir="ltr">import gromacs</p> <p dir="ltr">simulation = gromacs.MD(</p> <p dir="ltr"> molecule=protein_structure,</p> <p dir="ltr"> potential=mp2_potential,</p> <p dir="ltr"> integrator='verlet',</p> <p dir="ltr"> dt=0.1,</p> <p dir="ltr"> nsteps=100000</p> <p dir="ltr">)</p> <p dir="ltr">simulation.run()</p> <p dir="ltr"># Analyze the results</p> <p dir="ltr">results = simulation.get_results()</p> <p dir="ltr">print(results)</p> <p dir="ltr">Note that these are highly simplified examples, and in practice, more complex calculations and simulations would be required to obtain accurate results.</p> |
| title | CASPT2 and MP2 dynamics of the bionano interface |
| url | https://doi.org/10.5281/zenodo.17447408 |