I am attempting to create a simulation using gromacs based off of POPC128a.pdb and topol11885.top files that has 4 times the number of POP and Sol while maintaining all the other physical properties. Essentially, creating a POPC512a.pdb and topol47540.top to create a simulation. I know how to use editconf for the box size and a few other features, but I am new to gromacs and have looked through the documentation on how to possibly do this using editconf and other tools, but could not find a clear answer. Is there a simple way to make these changes? Or would I need to make these .pdb and .top files from scratch?
Thank you for any advice.
The tag "pdb-files" refers to "Program Database" files which are not related at all to the software gromacs and the world of bioinfromatics. Researchgate website might be more suitable.
You might want consult the gromacs resource/tutorial webpage which plenty of useful links.
You might replicate your simulation system coordinates with gmx genconf, and edit the topology file directly to specify the changed composition.
Related
I created my first Shiny app, which runs perfectly in my laptop.
However, I need to submit it to my professor and I want to make sure he will be able to run it.
I have a UI file, a server file, a global file and a process file.
The process file stores the data preparation.
The global file reads two RDS files which are the datasets that I use in the server.
Where should my libraries be loaded? For example, the app does not run without leaflet, how can I ensure the libraries are run automatically?
My RDS files are saved to my local drive, which means that my professor will need to change the path in order to use them, how can avoid this?
Shall I put the UI, server and global into one R script or is it ok to have them onto two different scripts?
Thank you!
As you describe your current set up, the most obvious place to load your libraries is at the start of your global file. (Or at the start of app.R if you move to a single file configuration.) Though not exactly what the reprex package is designed for, you could probably use reprex to make sure that your code is reproducible and independent of anything you may have overlooked. (You've already identified the obvious issue with data files.) Look here for more information on reprex.
Indeed. This is a problem. If you must load the data from files, you need to find a way of providing them to your professor. Telling him to edit your code by hand is not a good way to start. Exactly how to do this depends on the infrastucture your institution has set up, so it's difficult to advise you what to do. Do you not have a shared area for your course? Ask your fellow students - or even your professor.
Whether you bundle the app in a single file or in seperate files is really a matter of choice. I don't think there's a wroing way and a right way. For me, the deciding factor is usually the size of the app. Large apps get several files. For small apps, separation is just an unnecessary complication. Another factor - that doesn't seem to be an issue here - is whether I see the app as a potential front end for some methodology that might be worthy of its own package. In that case, I develop the app as a front end, and the package itself as separate entities.
Question 1 and 3 depend on criteria for code quality like performance and maintainability. When the code grows, there will come the point when it is more difficult to handle all code in one file. Once it grows even further you will encounter the point when you need split the app into modules to keep your code easy to maintain.
Regarding libraries I advise declaring them at the entrance point of an app (though, basically, that is a matter of taste and style). That way, you provide maximum clarity regarding the dependencies of the app. Again, if the app becomes very large and not all parts of the app rely on the same packages, it could improve performance and maintainability that each part loads the packages as required. It could give you a performance advantage when you do not need to load all packages at once. However, that is probably only true for very large apps.
However, since this all seems to be an exercise at university, I doubt that your app will reach higher levels of complexity.
Question 2: In a shiny app you can provide fileInput widget. This SO question shows you how.
I need to fix my Alloy graph, for example I have this output:
I can't move "node2" rectangle over the row of "node0" and "node1", and I can't move "node1" under "node2" whitout also move "node0". Is there any solution? Thank you.
PS: I am using Alloy Analyzer 4.2 under Windows.
PPS: This is only an example, i get a big graph with 5 or 6 rows of 20-25 rectangles, and if I can't fix it manually, it's only a mess.
To answer the direct question: I for one have never found a way to make the visualizer change its mind about which nodes should be on the same horizontal level. (That doesn't quite mean it's not possible, but it does mean that if it's possible it's not immediately obvious how to do it. But I guess you knew that already.)
If your goal is to make the auto-generated diagrams easier to read, the simplest approach is to experiment with adjustments to the visualizer theme. The "Magic Layout" button can be helpful; manual adjustments to hide some nodes or display some relations as labels rather than arcs can help with diagrams which are otherwise too cluttered.
If your goal is to make a 'good' version of a diagram for inclusion on a slide for a talk or a figure for a paper, you may want to export to Dot and import into a graph-drawing tool that gives you the kind of manual control you want (or edit the .dot file yourself, if you are familiar with graphviz and can make it do what you want), or export to XML and generate the graph description language of your choice from the XML.
I hope this helps.
The Lightning tool is an Ecplise plugin relying on Alloy4.2 to formally define Domain Specific Languages and might be a solution to your problem.
It's still under development, but if you are only interested in being able to freely reorganize each atom and label of generated instances, there shouldn't be any problems, as it uses Ecplise draw2D to render those latter.
If now you're really interested in providing an intuitive visualization to your generated instance (by intuitive I mean a visualization that is closer to its domain rather than the structure of your model), then you can define your own language (with your model as abstract syntax ) and define a concrete syntax for it.
The update site to be used for the installation of the tool is : http://lightning.gforge.uni.lu/update-site
Don't hesitate to contact me if you plan to give it a shot and get any issues.
(I'm eager of constructive feedbacks ;-) )
The steps to follow to generate a graphical instance in which any components can be moved are :
Install Lightning
Create a new Lightning Project
Create a new Language in this project
Put your model in the ASM folder
generate instances of the language by "running the project"
I'm looking for an online tools where me and my team could collaborate on creating graphs.
The purpose is to bind related words, and generate the adjacency list. For example,
Foo----Bar----Brool
|_____Lol
will generate the following list :
Foo,[Bar]
Bar,[Foo,Brool,Lol]
Brool,[Bar]
Lol,[Bar]
The idea is to allow people to collaborate simply using graph visualization, without diving through the adjacency list directly.
There is one service wchich I believe is going to be designed to allow people to collaborate on creating a graph. It is Graph Commons. Site slogan says:
Collaborative 'network mapping' platform and knowledge base of relationships
Unfortunately at the moment you can only sign up for beta invitation on the website. And from the website it is not clear what the creation/editing mechanism would be.
You could use yfiles library to build a graph editor online, but I've never used it and I don't know if you can manage multimple sessions (hence allowing direct collaboration). But, for instance, if you use graphity, which is an implementation of yfiles flex library, and save a file on dropbox, then each collaborator has access to that file, and you can set up a rudimentary collaboration graph tool. Maybe.
It would be great to have tools like LucidChart or Draw.io, but they don't allow to export a graph file (e.g. graphML from which you can then have an edgelist with some other programs like Gephi). Those tools only allow you to export images and vectors. Draw.io exports xml, but not graphML.
I believe Linkurious let you edit your graph. Again, I've never used it, I don't know if you can manage multiple sessions > collaboration. But I would check it out. Edit: Linkurious enterprise edition (see pricing) is desegned to handle multiple user sessions.
What about building something with vis.js? The library has the ability to «listen for changes in the data» using a DataSet component. Have a look at this example.
I'm sorry if I don't have any real answer, but since your question is very interesting in these days, and the right tools would come out sooner or later (if it doesn't exists), I wanted to share these thoughts. I hope they can help. Please post when you find a solution!
Current situation
My scientific project contains mainly different analytical and numerical calculations with physics purpose, i.e. I work with Mathematica, MATLAB, Fortran. Of course it is a good idea to commit the progress with a version control program like git.
I was asking some friends what would be the best way to structure my files. Beside the simple and well-known programmer's file structure (/bin/,/dat/,/doc/,/src/,...), I found no satisfying but similar answers:
What is the best project structure for a Python application?
Directory structure for a C++ library
Web Application (Django) typical project folder structure
Proper folder structure for lots of source files
https://stackoverflow.com/q/7715704/2062965
I hope this issue is not getting closed as it is asked by a physicist ;) as I guess many scientists are facing the same question at some point in more or less extension. By knowing that programmers have faced such issues before, I do not ask this question at Physics Stack Exchange, where it could probably be marked as off-topic or too broad.
Example
In my last project I had the following global structure where I had some interaction between the different project items:
/External_Code_Contribution/
/Experimental_Data/
/Analytical_Calculations/
/Project_Issue_1/
/Project_Issue_5/
/Documentations/
/Thesis/
/Papers/
/Talks/
/Literature/
/Project_Organization/
/Numerical_Calculations/
/Project_Issue_1/
/SubIssue_A/
/SubIssue_B/
/SubIssue_C/
/Project_Issue_2/
/Project_Issue_3/
/Project_Issue_4/
/Project_Issue_6/
Description:
In this project I divided the files according their functionality (external contribution, exp. data, numerics, documentation,...) and then subdivided them according to their issue (what was calculated at that step) where each issue again contained subissues (e.g. for analogous calculations with a different data set) with source code, binaries and processed data (for simplicity all in the same directory).
Unfortunately in this approach I ether had to:
refer to the source code in the corresponding issue (danger of changing anything can lead to incompatibilities), or
copy the source code to each new issue (each source code file with same name but in a different folder could be different).
Question
Who faced this issue of structuring projects in directories? Please tell me your approach and the arguments that brought you to this structure!
(Possible addition: What should I keep in mind when I set up a file structure for a project as described above?)
If you do not completely understand the answer, please do not hesitate to ask instead of flagging. Thank you!
I'm building an application that parses text files that contain information about specific nodes with incoming ports and outgoing ports that are interconnected. Doing some research there are some libraries but none of them support the exact characteristics needed.
this is what I'm trying to build and any language will do: Python, Perl, .net, etc.
One of the libraries I have found is GoDiagaram Node Classes
http://www.nwoods.com/components/dotnet/features-nodes.htm
The idea is to have boxes like so, interconnected and I should be able to click on one of them and link it to a new sub-diagram with more boxes contained in the one clicked.
Is there a counter part of these kind of charts that is opensource? and do these diagrams have a specific kind of name?
I don't know any specific details, since I never looked into this too closely, but here are some potential directions:
The data structure used for representing something like this is usually a graph (probably a directed graph). You could also try searching for graphical (or visual) programming languages. I seem to remember Pure Data as one that was relevant, but I never looked at it in detail.
Blender and VirtualDub both have a mode that's similar to this (the node editor and audio filters, respectively) and I believe both are open source, although I think neither has the option of having the nodes contain other nodes internally.
You could just use LabVIEW, which gives you the ability to create and edit LV code programmatically (search for "VI scripting"), but the code for that might not be very pretty and it's certainly not open source.