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master's thesis
Parametrizacija malih molekula u CHARMM polju sile
2019. urn:nbn:hr:166:392677
Goić, Renzo
University of Split
Faculty of Science
Department of Physics

Cite this document

Goić, R. (2019). Parametrizacija malih molekula u CHARMM polju sile (Master's thesis). Split: University of Split, Faculty of Science. Retrieved from https://urn.nsk.hr/urn:nbn:hr:166:392677

Goić, Renzo. "Parametrizacija malih molekula u CHARMM polju sile." Master's thesis, University of Split, Faculty of Science, 2019. https://urn.nsk.hr/urn:nbn:hr:166:392677

Goić, Renzo. "Parametrizacija malih molekula u CHARMM polju sile." Master's thesis, University of Split, Faculty of Science, 2019. https://urn.nsk.hr/urn:nbn:hr:166:392677

Goić, R. (2019). 'Parametrizacija malih molekula u CHARMM polju sile', Master's thesis, University of Split, Faculty of Science, accessed 19 April 2024, https://urn.nsk.hr/urn:nbn:hr:166:392677

Goić R. Parametrizacija malih molekula u CHARMM polju sile [Master's thesis]. Split: University of Split, Faculty of Science; 2019 [cited 2024 April 19] Available at: https://urn.nsk.hr/urn:nbn:hr:166:392677

R. Goić, "Parametrizacija malih molekula u CHARMM polju sile", Master's thesis, University of Split, Faculty of Science, Split, 2019. Available at: https://urn.nsk.hr/urn:nbn:hr:166:392677

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Metadata
TitleParametrizacija malih molekula u CHARMM polju sile
Title (english)Parametrization of small molecules in the CHARMM force field
AuthorRenzo Goić
MentorŽeljka Sanader Maršić (mentor)
Committee memberŽeljka Sanader Maršić (predsjednik povjerenstva)
Committee memberLarisa Zoranić (član povjerenstva)
Committee memberŽarko Kovač (član povjerenstva)
GranterUniversity of Split
Faculty of Science
(Department of Physics)
Split
Defense date and country2019-10-31, Croatia
Scientific / art field,
discipline and subdiscipline		NATURAL SCIENCES
Physics
Abstract
Simulacije molekularne dinamike su jedna od najznačajnih biofizikalnih metoda za istraživanje bioloških sustava na atomskoj razini. Uz zadane početne strukture molekula, za opis sustava, važno je definirati parametre polja sile. Polje sila CHARMM General Force Field (CgenFF) sadrži parametre za opis međudjelovanja malih molekula. Razvoj CHARMM General Force Fielda pridonio je razvitku parametrizacijskog alata Force Field Toolkit (ffTK) koji je dio programskog paketa za vizualizaciju podataka iz simulacija molekularne dinamike Visual Molecular Dynamics (VMD). Force Field Toolkit, s njegovim grafičkim korisničkim sučeljem koje prati jasno određen parametrizacijski tijek rada, olakšava i ubrzava ab initio razvoj parametara. U ovom radu izložena je teoretska osnova Force Field Toolkit parametrizacijskog alata i pokazana je njegova primjena na dvije male molekule 1-propanol i metoksibenzen (anisol).
Abstract (english)
Molecular dynamics simulations are one of the most important biophysical methods for studying biological systems on the atomic level. For description of system, with initial molecular structures, it is important to define force field parameters. CHARMM General Force Field (CGenFF) contains parameters for description of small molecules interactions. Development of CHARMM General Force Field contributed to development of Force Field Toolkit (ffTK) parametrization tool as an add-on for Visual Molecular Dynamics (VMD) program for data visualization from molecular dynamics simulations. Force Field Toolkit, with it's graphical user interface that follows well defined parameterization workflow, simplifies ab initio parameter development. Herein, theoretical basics of Force Field Toolkit parameterization tool are described and it's application on two small molecules, 1-propanol and methoxybenzene (anisole), is shown.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:166:392677
Study programmeTitle: Physics; specializations in: major in teaching, major in Astrophysics, major in Biophysics, major in Enviromental physics, major in Computational physics
Course: major in Biophysics
Study programme type: university
Study level: graduate
Academic / professional title: magistar/magistra fizike (magistar/magistra fizike)
Type of resourceText
File originBorn digital
Access conditionsAccess restricted to authenticated users
Terms of useLicence In copyright icon
Created on2019-11-06 09:23:04