A penalty function method for constrained molecular dynamics

dc.contributor.advisor	Zhjun Wu
dc.contributor.author	Gunaratne, Ajith
dc.contributor.department	Mathematics
dc.date	2018-08-24T20:49:09.000
dc.date.accessioned	2020-06-30T07:42:33Z
dc.date.available	2020-06-30T07:42:33Z
dc.date.copyright	Sun Jan 01 00:00:00 UTC 2006
dc.date.issued	2006-01-01
dc.description.abstract	<p>We propose a penalty-function method for constrained molecular dynamic simulation by defining a quadratic penalty function for the constraints. The simulation with such a method can be done by using a conventional, unconstrained solver only with the penalty parameter increased in an appropriate manner as the simulation proceeds. More specifically, we scale the constraints with their force constants when forming the penalty terms. The resulting force function can then be viewed as a smooth continuation of the original force field as the penalty parameter increases. The penalty function method is easy to implement and costs less than a Lagrange multiplier method, which requires the solution of a nonlinear system of equations in every time step. We have first implemented a penalty function method in CHARMM and applied it to protein Bovine Pancreatic Trypsin Inhibitor (BPTI). We compared the simulation results with Verlet and Shake, and found that the penalty function method had high correlations with Shake and outperformed Verlet. In particular, the RMSD fluctuations of backbone and non-backbone atoms and the velocity auto correlations of Ca atoms of the protein calculated by the penalty function method agreed well with those by Shake. We have also tested the method on a group of argon clusters constrained with a set of inter-atomic distances in their global energy minimum states. The results showed that the method was able to impose the constraints effectively and the clusters tended to converge to their energy minima more rapidly than not confined by the constraints.</p>
dc.format.mimetype	application/pdf
dc.identifier	archive/lib.dr.iastate.edu/rtd/1519/
dc.identifier.articleid	2518
dc.identifier.contextkey	6094955
dc.identifier.doi	https://doi.org/10.31274/rtd-180813-12123
dc.identifier.s3bucket	isulib-bepress-aws-west
dc.identifier.submissionpath	rtd/1519
dc.identifier.uri	https://dr.lib.iastate.edu/handle/20.500.12876/68797
dc.language.iso	en
dc.source.bitstream	archive/lib.dr.iastate.edu/rtd/1519/r_3229080.pdf\|\|\|Fri Jan 14 20:36:58 UTC 2022
dc.subject.disciplines	Biophysics
dc.subject.disciplines	Mathematics
dc.subject.disciplines	Molecular Biology
dc.subject.keywords	Mathematics
dc.subject.keywords	Applied mathematics
dc.title	A penalty function method for constrained molecular dynamics
dc.type	article
dc.type.genre	dissertation
dspace.entity.type	Publication
relation.isOrgUnitOfPublication	82295b2b-0f85-4929-9659-075c93e82c48
thesis.degree.level	dissertation
thesis.degree.name	Doctor of Philosophy

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