Lessons learned about steered molecular dynamics simulations and free energy calculations
The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM-MM tools, ligand migration, and conformational rearrangements that can be modeled using classical potentials. The use of steered molecular d...
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2019
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17470277_v_n_p_Boubeta http://hdl.handle.net/20.500.12110/paper_17470277_v_n_p_Boubeta |
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paper:paper_17470277_v_n_p_Boubeta2023-06-08T16:28:27Z Lessons learned about steered molecular dynamics simulations and free energy calculations free energy Jarzynski maximum likelihood steered molecular dynamics The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM-MM tools, ligand migration, and conformational rearrangements that can be modeled using classical potentials. The use of steered molecular dynamics (sMD) together with the Jarzynski equality is a popular approach in calculating free energy profiles. Here, we first briefly review the application of the Jarzynski equality to sMD simulations, then revisit the so-called stiff-spring approximation and the consequent expectation of Gaussian work distributions and, finally, reiterate the practical utility of the second-order cumulant expansion, as it coincides with the parametric maximum-likelihood estimator in this scenario. We illustrate this procedure using simulations of CO, both in aqueous solution and in a carbon nanotube as a model system for biologically relevant nanoheterogeneous environments. We conclude the use of the second-order cumulant expansion permits the use of faster pulling velocities in sMD simulations, without introducing bias due to large dispersion in the non-equilibrium work distribution. © 2019 John Wiley & Sons A/S 2019 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17470277_v_n_p_Boubeta http://hdl.handle.net/20.500.12110/paper_17470277_v_n_p_Boubeta |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
free energy Jarzynski maximum likelihood steered molecular dynamics |
| spellingShingle |
free energy Jarzynski maximum likelihood steered molecular dynamics Lessons learned about steered molecular dynamics simulations and free energy calculations |
| topic_facet |
free energy Jarzynski maximum likelihood steered molecular dynamics |
| description |
The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM-MM tools, ligand migration, and conformational rearrangements that can be modeled using classical potentials. The use of steered molecular dynamics (sMD) together with the Jarzynski equality is a popular approach in calculating free energy profiles. Here, we first briefly review the application of the Jarzynski equality to sMD simulations, then revisit the so-called stiff-spring approximation and the consequent expectation of Gaussian work distributions and, finally, reiterate the practical utility of the second-order cumulant expansion, as it coincides with the parametric maximum-likelihood estimator in this scenario. We illustrate this procedure using simulations of CO, both in aqueous solution and in a carbon nanotube as a model system for biologically relevant nanoheterogeneous environments. We conclude the use of the second-order cumulant expansion permits the use of faster pulling velocities in sMD simulations, without introducing bias due to large dispersion in the non-equilibrium work distribution. © 2019 John Wiley & Sons A/S |
| title |
Lessons learned about steered molecular dynamics simulations and free energy calculations |
| title_short |
Lessons learned about steered molecular dynamics simulations and free energy calculations |
| title_full |
Lessons learned about steered molecular dynamics simulations and free energy calculations |
| title_fullStr |
Lessons learned about steered molecular dynamics simulations and free energy calculations |
| title_full_unstemmed |
Lessons learned about steered molecular dynamics simulations and free energy calculations |
| title_sort |
lessons learned about steered molecular dynamics simulations and free energy calculations |
| publishDate |
2019 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17470277_v_n_p_Boubeta http://hdl.handle.net/20.500.12110/paper_17470277_v_n_p_Boubeta |
| _version_ |
1768543868902440960 |