colvars | Collective variables module for molecular simulation

by Colvars C++ Version: lammps-stable_23Jun2022 License: LGPL-3.0

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | colvars Summary

colvars is a C++ library typically used in Simulation applications. colvars has no bugs, it has no vulnerabilities, it has a Weak Copyleft License and it has low support. You can download it from GitHub.

A software module for molecular simulation and analysis that provides a high-performance implementation of sampling algorithms defined on a reduced space of continuously differentiable functions (aka collective variables). First released in 2008 as part of the standard distribution of NAMD version 2.7b1, Colvars has also been integrated in LAMMPS and VMD. Pre-patched GROMACS releases are also available (see below). The module itself implements a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions.

Support

Quality

Security

License

Reuse

Support

colvars has a low active ecosystem.

It has 155 star(s) with 48 fork(s). There are 17 watchers for this library.

It had no major release in the last 6 months.

There are 17 open issues and 282 have been closed. On average issues are closed in 244 days. There are 4 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of colvars is lammps-stable_23Jun2022

Quality

colvars has no bugs reported.

Security

colvars has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

colvars is licensed under the LGPL-3.0 License. This license is Weak Copyleft.

Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

Reuse

colvars releases are not available. You will need to build from source code and install.

Installation instructions are not available. Examples and code snippets are available.

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colvars Key Features

No Key Features are available at this moment for colvars.

colvars Examples and Code Snippets

No Code Snippets are available at this moment for colvars.

Community Discussions

Trending Discussions on colvars

In R, how can I italicize part of a label that I display on only some tiles of a correlation matrix using ggplot

order data.table with dash in column name || error Error in .checkTypos - Perhaps you intended

Using summarize_all with colMeans and colVar to create pivoted table in R

Programming with Dplyr: How to make a function that can be used in a for loop?

System.OutOfMemoryException and complication with Using StringBuilder

QUESTION

In R, how can I italicize part of a label that I display on only some tiles of a correlation matrix using ggplot

Asked 2021-Feb-05 at 21:59

Using ggplot, I want to create a correlation matrix where some of the tiles are labeled with the p-value. Within those tiles, I want the "p" to be italicized.

This is plot that I want, except the "p"s should be italicized.

Right now, I am using the aes(label) to fill the tiles, and creating those labels outside of the plot. That way, I could just create blank labels to be displayed inside the plot.

The plot is currently made using:

...

ANSWER

Answered 2021-Feb-05 at 21:59

This should work (use italic() along with a plotmath expression and parse=TRUE in geom_text()):

Source https://stackoverflow.com/questions/66067794

QUESTION

order data.table with dash in column name || error Error in .checkTypos - Perhaps you intended

Asked 2020-Nov-24 at 20:45

create sample data.table

...

ANSWER

Answered 2020-Nov-24 at 18:45

In R you always need to use backticks `` when the name isn't regular, or use the get function or eval-as.name

Source https://stackoverflow.com/questions/64992833

QUESTION

Using summarize_all with colMeans and colVar to create pivoted table in R

Asked 2020-May-21 at 00:39

I want to use summarize_all on the following data and create my desired output, but I was curious how to do this the tidy way using some combination of mutate and summarize I think? Any help appreciated!!

...

ANSWER

Answered 2020-May-21 at 00:39

It would be easier to reshape to 'long' format and then do it once after grouping by 'name'

Source https://stackoverflow.com/questions/61925241

QUESTION

Programming with Dplyr: How to make a function that can be used in a for loop?

Asked 2018-Mar-08 at 15:11

Goal

I'm trying to create a function that creates a custom cross table (a.k.a. pivot table). To do this I'm using the rlang package, trying to stick to the "dplyr" way of programming. See also http://dplyr.tidyverse.org/articles/programming.html.

The function

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ANSWER

Answered 2018-Mar-08 at 15:11

An option would be to convert the 'expr' to quosures and then within the loop, evaluate the arguments with !! along with conversion of character vector ('colVars') to sym ('symbol')

Source https://stackoverflow.com/questions/49173984

QUESTION

System.OutOfMemoryException and complication with Using StringBuilder

Asked 2017-Jun-21 at 06:14

The following code give me System.OutOfMemoryException and i tried to change it by using StringBuilder in my code but i couldn't succeed in using it.

anyone can tell me what is the best approach to use StringBuilder instead of many concatenations between strings in my code?

...

ANSWER

Answered 2017-Jun-20 at 20:57

The problem is in these lines:

Source https://stackoverflow.com/questions/44654063

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install colvars

You can download it from GitHub.

Support

The Colvars webpage includes user documentation for the four codes, as well as a Doxygen-based developer documentation. The reference article is: G. Fiorin, M. L. Klein, and J. Hénin, Molecular Physics 111, 3345 (2013). https://dx.doi.org/10.1080/00268976.2013.813594 [BibTex file] [Endnote file].

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