Molecular Dynamics at Constant Pressure: Allowing the System to Control Volume Fluctuations via a “Shell” Particle
Since most experimental observations are performed at constant temperature and pressure, the isothermal-isobaric (NPT) ensemble has been widely used in molecular simulations. Nevertheless, the NPT ensemble has only recently been placed on a rigorous foundation. The proper formulation of the NPT ense...
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| Format: | Article |
| Language: | English |
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MDPI AG
2013-09-01
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| Series: | Entropy |
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| Online Access: | http://www.mdpi.com/1099-4300/15/9/3941 |
| _version_ | 1811304857022234624 |
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| author | David S. Corti Mark J. Uline |
| author_facet | David S. Corti Mark J. Uline |
| author_sort | David S. Corti |
| collection | DOAJ |
| description | Since most experimental observations are performed at constant temperature and pressure, the isothermal-isobaric (NPT) ensemble has been widely used in molecular simulations. Nevertheless, the NPT ensemble has only recently been placed on a rigorous foundation. The proper formulation of the NPT ensemble requires a “shell” particle to uniquely identify the volume of the system, thereby avoiding the redundant counting of configurations. Here, we review our recent work in incorporating a shell particle into molecular dynamics simulation algorithms to generate the correct NPT ensemble averages. Unlike previous methods, a piston of unknown mass is no longer needed to control the response time of the volume fluctuations. As the volume of the system is attached to the shell particle, the system itself now sets the time scales for volume and pressure fluctuations. Finally, we discuss a number of tests that ensure the equations of motion sample phase space correctly and consider the response time of the system to pressure changes with and without the shell particle. Overall, the shell particle algorithm is an effective simulation method for studying systems exposed to a constant external pressure and may provide an advantage over other existing constant pressure approaches when developing nonequilibrium molecular dynamics methods. |
| first_indexed | 2024-04-13T08:14:48Z |
| format | Article |
| id | doaj.art-72272b1e3501410f92c46124a1cd27d9 |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-04-13T08:14:48Z |
| publishDate | 2013-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-72272b1e3501410f92c46124a1cd27d92022-12-22T02:54:49ZengMDPI AGEntropy1099-43002013-09-011593941396910.3390/e15093941Molecular Dynamics at Constant Pressure: Allowing the System to Control Volume Fluctuations via a “Shell” ParticleDavid S. CortiMark J. UlineSince most experimental observations are performed at constant temperature and pressure, the isothermal-isobaric (NPT) ensemble has been widely used in molecular simulations. Nevertheless, the NPT ensemble has only recently been placed on a rigorous foundation. The proper formulation of the NPT ensemble requires a “shell” particle to uniquely identify the volume of the system, thereby avoiding the redundant counting of configurations. Here, we review our recent work in incorporating a shell particle into molecular dynamics simulation algorithms to generate the correct NPT ensemble averages. Unlike previous methods, a piston of unknown mass is no longer needed to control the response time of the volume fluctuations. As the volume of the system is attached to the shell particle, the system itself now sets the time scales for volume and pressure fluctuations. Finally, we discuss a number of tests that ensure the equations of motion sample phase space correctly and consider the response time of the system to pressure changes with and without the shell particle. Overall, the shell particle algorithm is an effective simulation method for studying systems exposed to a constant external pressure and may provide an advantage over other existing constant pressure approaches when developing nonequilibrium molecular dynamics methods.http://www.mdpi.com/1099-4300/15/9/3941isothermal-isobaric ensemblemolecular dynamics |
| spellingShingle | David S. Corti Mark J. Uline Molecular Dynamics at Constant Pressure: Allowing the System to Control Volume Fluctuations via a “Shell” Particle Entropy isothermal-isobaric ensemble molecular dynamics |
| title | Molecular Dynamics at Constant Pressure: Allowing the System to Control Volume Fluctuations via a “Shell” Particle |
| title_full | Molecular Dynamics at Constant Pressure: Allowing the System to Control Volume Fluctuations via a “Shell” Particle |
| title_fullStr | Molecular Dynamics at Constant Pressure: Allowing the System to Control Volume Fluctuations via a “Shell” Particle |
| title_full_unstemmed | Molecular Dynamics at Constant Pressure: Allowing the System to Control Volume Fluctuations via a “Shell” Particle |
| title_short | Molecular Dynamics at Constant Pressure: Allowing the System to Control Volume Fluctuations via a “Shell” Particle |
| title_sort | molecular dynamics at constant pressure allowing the system to control volume fluctuations via a shell particle |
| topic | isothermal-isobaric ensemble molecular dynamics |
| url | http://www.mdpi.com/1099-4300/15/9/3941 |
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