IRCCAR: Difference between revisions
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# | The {{FILE|IRCCAR}} file defines a discretized transformation path. Usually this is taken from an [[Intrinsic-reaction-coordinate calculations|intrinsic reaction coordinate]] (IRC) - using {{TAG|IBRION}}=40, projected onto a small set of internal coordinates. It is required to define the path-based coordinates <code>IS</code> and <code>IZ</code> in [[ICONST#In_case_of_complex_coordinates|ICONST]] {{Cite|branduari:parrinello:2007}}. | ||
However, this path is followed during a biased molecular dynamics (MD) simulation, similar to the [[Blue moon ensemble]] method, [[Metadynamics|metadynamics]], and other [[:Category:Advanced molecular-dynamics sampling| advanced MD aproaches]] {{Cite|bucko:book:2025}}. The structure of the file is: | |||
M | |||
chi_1(1) chi_2(1) ... chi(r)(1) | |||
chi_1(2) chi_2(2) ... chi(r)(2) | |||
... | |||
chi_1(M) chi_2(M) ... chi(r)(M) | |||
where <code>M</code> is the number of points in the file and <code>chi_j(i)</code> is <math>\tilde{\chi}_k(i)</math>, the discretized transformation path in terms of internal coordinates, taking values between 0 and 1. | |||
{{NB|mind|Contact [https://fns.uniba.sk/en/tomas-bucko/ Tomáš Bučko] for necessary Python scripts to prepare this file.}} | |||
==Related tags and articles== | |||
{{FILE|ICONST}} | |||
==References== | |||
[[Category:Files]][[Category:Input files]][[Category:Advanced molecular-dynamics sampling]][[Category:Biased molecular dynamics]][[Category:Transition states]] | |||
Latest revision as of 10:32, 19 June 2026
The IRCCAR file defines a discretized transformation path. Usually this is taken from an intrinsic reaction coordinate (IRC) - using IBRION=40, projected onto a small set of internal coordinates. It is required to define the path-based coordinates IS and IZ in ICONST [1].
However, this path is followed during a biased molecular dynamics (MD) simulation, similar to the Blue moon ensemble method, metadynamics, and other advanced MD aproaches [2]. The structure of the file is:
M chi_1(1) chi_2(1) ... chi(r)(1) chi_1(2) chi_2(2) ... chi(r)(2) ... chi_1(M) chi_2(M) ... chi(r)(M)
where M is the number of points in the file and chi_j(i) is [math]\displaystyle{ \tilde{\chi}_k(i) }[/math], the discretized transformation path in terms of internal coordinates, taking values between 0 and 1.
| Mind: Contact Tomáš Bučko for necessary Python scripts to prepare this file. |