SPRING V0: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
{{DISPLAYTITLE:SPRING_V0}} | {{DISPLAYTITLE:SPRING_V0}} | ||
{{TAGDEF|SPRING_V0|[real (array)]}} | {{TAGDEF|SPRING_V0|[real (array)]}} | ||
{{DEF|SPRING_V0|0|for all coordinates with <code>status{{=}}8</code> in {{FILE|ICONST}}.}} | |||
Description: Consider the bias potential of the form: | Description: Rate at which the bias potential is shifted in <math>uc/fs</math>. | ||
---- | |||
Consider the bias potential for a [[:Category:Molecular dynamics|molecular-dynamics]] (MD) run of the form: | |||
<math> | ::<math> | ||
\tilde{V}(\xi_1,\dots,\xi_{M_8}) = \sum_{\mu=1}^{ | \tilde{V}(\xi_1,\dots,\xi_{M_8}) = \sum_{\mu=1}^{M_8}\frac{1}{2}\kappa_{\mu} (\xi_{\mu}(q)-\xi_{0\mu})^2, \; | ||
</math> | </math> | ||
where the sum runs over all (<math>M_8</math>) coordinates | where the sum runs over all (<math>M_8</math>) coordinates the potential acts upon (<math>\xi_{\mu}(q)</math>). The coordinates are defined in the {{FILE|ICONST}} file by setting the <code>status=8</code>. | ||
Optionally, the position of minimum (<math>\xi_{0\mu}</math>) can be shifted | Optionally, the position of minimum (<math>\xi_{0\mu}</math>) can be shifted at a constant rate <math>\dot{\xi}_{\mu}</math> every MD step, i.e., | ||
<math> | ::<math> | ||
\xi_{0\mu}(t+\Delta t) = \xi_{0\mu}(t) + \dot{\xi}_{\mu}(q)\Delta t \; | \xi_{0\mu}(t+\Delta t) = \xi_{0\mu}(t) + \dot{\xi}_{\mu}(q)\Delta t, \; | ||
</math> | </math> | ||
| Line 18: | Line 21: | ||
The rate <math>\dot{\xi}_{\mu}</math> can be defined via the parameter {{TAG|SPRING_V0}} and its units are <math>uc/fs</math>, where <math>uc</math> corresponds to the units of the coordinate the potential acts upon (e.g., <math>{\AA}</math> for coordinates with <code>flag</code> R, <math>rad.</math> for coordinates with <code>flag</code> A, dimensionless for coordinates with <code>flag</code> W, etc...). | The rate <math>\dot{\xi}_{\mu}</math> can be defined via the parameter {{TAG|SPRING_V0}} and its units are <math>uc/fs</math>, where <math>uc</math> corresponds to the units of the coordinate the potential acts upon (e.g., <math>{\AA}</math> for coordinates with <code>flag</code> R, <math>rad.</math> for coordinates with <code>flag</code> A, dimensionless for coordinates with <code>flag</code> W, etc...). | ||
The number of items defined via {{TAG|SPRING_V0}} must be equal to <math>M_8</math>, otherwise the calculation terminates with an error message. | The number of items defined via {{TAG|SPRING_V0}} must be equal to <math>M_8</math>, otherwise the calculation terminates with an error message. | ||
== Related tags and articles == | == Related tags and articles == | ||
{{TAG|SPRING_K}} | {{TAG|SPRING_K}}, | ||
{{TAG|SPRING_R0}} | {{TAG|SPRING_R0}}, | ||
{{FILE|ICONST}} | {{FILE|ICONST}}, | ||
{{TAG|Biased molecular dynamics}} | {{TAG|Biased molecular dynamics}} | ||
---- | |||
[[Category:Molecular dynamics]][[Category:Biased molecular dynamics]] | |||
Revision as of 06:58, 24 April 2023
SPRING_V0 = [real (array)]
| Default: SPRING_V0 | = 0 | for all coordinates with status=8 in ICONST.
|
Description: Rate at which the bias potential is shifted in [math]\displaystyle{ uc/fs }[/math].
Consider the bias potential for a molecular-dynamics (MD) run of the form:
- [math]\displaystyle{ \tilde{V}(\xi_1,\dots,\xi_{M_8}) = \sum_{\mu=1}^{M_8}\frac{1}{2}\kappa_{\mu} (\xi_{\mu}(q)-\xi_{0\mu})^2, \; }[/math]
where the sum runs over all ([math]\displaystyle{ M_8 }[/math]) coordinates the potential acts upon ([math]\displaystyle{ \xi_{\mu}(q) }[/math]). The coordinates are defined in the ICONST file by setting the status=8.
Optionally, the position of minimum ([math]\displaystyle{ \xi_{0\mu} }[/math]) can be shifted at a constant rate [math]\displaystyle{ \dot{\xi}_{\mu} }[/math] every MD step, i.e.,
- [math]\displaystyle{ \xi_{0\mu}(t+\Delta t) = \xi_{0\mu}(t) + \dot{\xi}_{\mu}(q)\Delta t, \; }[/math]
where [math]\displaystyle{ \Delta t }[/math] is the time step used in MD (POTIM).
The rate [math]\displaystyle{ \dot{\xi}_{\mu} }[/math] can be defined via the parameter SPRING_V0 and its units are [math]\displaystyle{ uc/fs }[/math], where [math]\displaystyle{ uc }[/math] corresponds to the units of the coordinate the potential acts upon (e.g., [math]\displaystyle{ {\AA} }[/math] for coordinates with flag R, [math]\displaystyle{ rad. }[/math] for coordinates with flag A, dimensionless for coordinates with flag W, etc...).
The number of items defined via SPRING_V0 must be equal to [math]\displaystyle{ M_8 }[/math], otherwise the calculation terminates with an error message.
Related tags and articles
SPRING_K, SPRING_R0, ICONST, Biased molecular dynamics