A new constant pressure algorithm and periodic boundary conditions in molecular dynamics free energy calculations.

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(1)UPTEC X 02 012 MAR 2002. ISSN 1401-2138. PETRA WENNERSTRÖM. A new constant pressure algorithm and periodic boundary conditions in molecular dynamics free energy calculations. Master’s degree project.

(2) Molecular Biotechnology Programme Uppsala University School of Engineering Date of issue 2002-03. UPTEC X 02 012 Author. Petra Wennerström Title (English). A new constant pressure algorithm and periodic boundary conditions in molecular dynamics free energy calculations Title (Swedish) Abstract Periodic boundary conditions were implemented in a already existing molecular dynamics software. In addition a new constant pressure algorithm was implemented. The new algorithm is a combination of molecular dynamics and Monte Carlo volume sampling. The results are promising but the algorithm needs more testing. Keywords Molecular dynamics, periodic boundary conditions, isothermal- isobaric ensemble, Monte Carlo, constant pressure. Supervisor. Johan Åqvist Uppsala University Examiner. David van der Spoel Uppsala University Project name. Sponsors. Language. Security. English Classification. ISSN 1401-2138 Supplementary bibliographical information. Pages. 20 Biology Education Centre Box 592 S-75124 Uppsala. Biomedical Center Tel +46 (0)18 4710000. Husargatan 3 Uppsala Fax +46 (0)18 555217.

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