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kandi X-RAY | GROMACS Summary
kandi X-RAY | GROMACS Summary
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Top functions reviewed by kandi - BETA
- Set resname check coordinates
- Get the output of a command
- Prints quoted text
- Compute the distance between two vectors
- Create the mol topol file
- Save to pickle file
- Writes the charsums to the molecule
- Get the residue label
- Creates the acorn
- Checks the given log
- Removes temporary output files
- Execute Sleap
- Get the atoms
- Returns a list of ACOefs
- A helper method to balance a charge list
- Get the data for a given flag
- Signal handler for SIGM
- Get the family family of a given job
- Try to guess the charge
- Return the total charge of a mol2 file
- Returns a list of all dihedrals
- Returns a list of angles
- Set atom pairs
- Returns a list of Bond objects
- Get excluded atoms
- Print invalid arguments
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Community Discussions
Trending Discussions on GROMACS
QUESTION
I use GROMACS. I think about how can I make my script faster. This is my script
...ANSWER
Answered 2021-Jun-03 at 15:17Terminals have 3 file descriptors by default:
- Standard input, a.k.a.
stdin - Standard output, a.k.a.
stdout - Standard error, a.k.a.
stderr
When redirecting >/dev/null it actually redirects the standard output to /dev/null, which is strictly equivalent to 1>/dev/null
However the program may also output to the standard error, in which case you may want to add 2>/dev/null to suppress stderr messages:
QUESTION
I am running the following slurm script on a cluster computing system.
...ANSWER
Answered 2021-Mar-19 at 07:15You have a missing } in the line
QUESTION
I have a data file which looks like::
...ANSWER
Answered 2021-Mar-16 at 01:17It is a one-liner in python. Something like:
QUESTION
I am trying to implement some sort of Master-Worker system in a HPC with the resource manager SLURM, and I am looking for advices on how to implement such a system.
I have to use some python code that plays the role of the Master, in the sense that between batches of calculations the Master will run 2 seconds of its own calculations, before sending a new batch of work to the Workers. Each Worker must run an external executable over a single node of the HPC. The external executable (Gromacs) is itself MPI-enabled. There will be ~25 Workers and many batches of calculations.
What I have in mind atm (also see EDIT further below): What I'm currently trying:- Allocate via SLURM as many MPI tasks as I want to use nodes, within a bash script that I'm calling via
sbatch run.sh
ANSWER
Answered 2021-Feb-16 at 04:31At first glance, this looks over convoluted to me:
- there is no communication between a slave and GROMACS
- there is some master/slave communications, but is MPI really necessary?
- are the slaves really necessary? (e.g. can the master process simply serialize the computation and then directly start GROMACS?)
A much simpler architecture would be to have one process on your frontend, that will do:
- prepare the GROMACS inputs
sbatch gromacs(start several jobs in a row)- wait for the GROMACS jobs to complete
- analyze the GROMACS outputs
- re-iterate or exit
If the slave is doing some work you do not want to serialize on the master, can you replace the MPI communications by using files on a shared filesystem? in that case, you can do the computation on the compute nodes within a GROMACS job, before and after executing GROMACS. If not, maybe TCP/IP based communications can do the trick.
QUESTION
I'm attempting to install GROMACS on Linux for my Masters Project. I've followed the instructions given in this guide https://github.com/rehanzfr/MDSimulations/blob/master/README.md, I’ve gotten to nearly the final step, running the line:
sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_C_COMPILER=gcc -DREGRESSIONTEST_PATH=/home/username/Downloads/GromacsDownload/regressiontests-2020
However I’ve fallen at the final hurdle and I’m getting the error:
...ANSWER
Answered 2021-Feb-14 at 09:09I don't know what GROMACS but probably the following will shine a little light on it.
Doxygen is in principle not a library but a program that has to be installed, so either a version is available for you platform (might not be the most current version of doxygen though, the current version is 1.9.1) and you can install it directly by means of an apt-get call otherwise you have to download a the sources from https://www.doxygen.nl/download.html or get the sources directly from the repository at https://github.com/doxygen/doxygen. After you have the sources you can build with cmake / make / install your doxygen version and use it.
QUESTION
I would like to know whether it is possible, and how, to host a Jupyter Notebook page somewhere remotely (so not on my machine) that a collaborator could load in their web browser to view results? There is no shared machine, all the files need to be in one central location e.g., hosted on Google Drive, and the Jupyter Notebook page must also be URL based accessible.
First of all, I've performed MD simulations using Gromacs and the files are currently local on my machine. I then load Jupyter Notebook on my machine, import the MDAnalysis Python package and perform some analysis that depends on those trajectory files generated by Gromacs (.trr/.xtc/.pdb). I also include some short simulation trajectories using NGLViewer so I can observe the parts of a simulation.
The problem I face is that I want my collaborator to see/interact with the analysis work and observe the simulations using NGLViewer.
There are a few challenges involved:
(1) How/where do I host a Jupyter Notebook remotely so my collaborator can view progress in a browser window? I'm not expecting them to make edits or run code, just observe and copy text and download figures. This is to save me from packaging (e.g., as a markdown document of some kind) incremental versions of analysis and emailing them over.
(2) What is required for analysis code (written in Python and using the MDAnalysis package) in this remote Jupyter Notebook page to load data files that are stored remotely on e.g., Google Drive?
(3) Similar to (2), can NGLViewer load a remote file e.g., stored on Google Drive, and display the trajectory on the site for the collaborator to observe?
Although my question ties in python packages such as MDAnalysis, NGLViewer and the results from a third party application (Gromacs), I'm looking for a new way sharing results from multiple projects to teams in different countries, along with my own team who I can't meet in person at the moment.
...ANSWER
Answered 2021-Jan-27 at 11:43You can create a Google Drive folder and add the data to it. Then share the data with all your colleagues that need to access the data.
Finally, create a Google Colab notebook and add the code there. You can choose to allow people to edit and run the notebook or only allow them to see the results. If you only give them read permission, they will have to save a copy from the notebook into their own google drive to be allowed to edit the notebook.
These options are all available in the menu bar from Colab.
You can connect your google drive folder to Colab as follows:
QUESTION
I try to make image remotely. I use Windows 7 and work remotely on Linux Ubuntu 16.04 by using WinSCP and Putty. I write in terminal
...ANSWER
Answered 2021-Jan-10 at 15:26Yeah I found an answer, I just delete replot and change order
QUESTION
I have a huge problem. I am working on .gro files, which looks like that:
...ANSWER
Answered 2020-Mar-14 at 14:27The script you posted doesn't produce the output you posted but if it did then here's what you'd change it to:
QUESTION
this is probably a very basic question. I am using the bash shell still (Catalina). And I downloaded gromacs. Every time I open a new terminal window I first have to put
...ANSWER
Answered 2019-Dec-01 at 06:18If you are still using the bash shell on macOS, all you have to do is:
Put the line:
QUESTION
I have the following code that is designed to carry out a simulation. Once the simulation is finished it will remove text from the output file and use the new edited output file as the input for a new simulation. What happens is I get stuck in a while loop regarding the existence of the GROPATH file. I get the following loop printed to the log file:
...ANSWER
Answered 2019-Jun-12 at 04:38The test [ ! -d "$GROPATH" ] checks for a directory by that name, not a file. To check for a file, use -f instead of -d (or just use -e, which'll check for anything by that name).
Other problems: while (grep -c SOL md$i.gro > 20); do doesn't do what you want; the () create a subshell which runs the grep command with its output redirected to a file named
"20". Use while [ "$(grep -c SOL md$i.gro)" -gt 20 ]; do instead.
Also, you have echo "waiting" sleep 10800 as a single command, so it prints the "sleep 10800" instead of executing it as a command; just move it to a separate line.
And the way you select i is a mess; try this instead:
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