Down for Everyone or Just Me

Oct 13, 2025 by wbrum.org 72 views

The md traj data cannot download now: Troubleshooting and Solutions

The inability to download molecular dynamics (MD) trajectory data can be frustrating, especially when it's essential for research or analysis. In this article, we'll explore the issue of md traj data not downloading, specifically focusing on the mdshare library and the ftp.imp.fu-berlin.de server. We'll delve into the error messages, potential causes, and provide solutions to overcome these challenges.

The error message you provided indicates a connection issue with the ftp.imp.fu-berlin.de server:

HTTPConnectionPool(host='ftp.imp.fu-berlin.de', port=80): Max retries exceeded with url: /pub/cmb-data/pentapeptide-impl-solv.pdb (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fdf0dd0c730>: Failed to establish a new connection: [Errno 113] No route to host'))

This error suggests that the connection to the server is being refused, likely due to a network issue or a problem with the server itself.

Since the ftp.imp.fu-berlin.de server is not accessible, we can try alternative download options. In this case, we can use the mdshare library to download the data from the website https://markovmodel.github.io/mdshare/pentapeptide/.

The mdshare library provides a convenient way to download MD trajectory data from various sources. To download the data, you can use the following code:

import mdshare

# Download the PDB file
pdb = mdshare.fetch('pentapeptide-impl-solv.pdb', working_directory='data')

# Download the XTC file
files = mdshare.fetch('pentapeptide-*-500ns-impl-solv.xtc', working_directory='data')

However, if the ftp.imp.fu-berlin.de server is not accessible, this code may not work.

To troubleshoot the issue, follow these steps:

Check the server status: Verify that the ftp.imp.fu-berlin.de server is up and running. You can use online tools like Down for Everyone or Just Me to check the server status.
Check the network connection: Ensure that your network connection is stable and working properly.
Check the mdshare library version: Make sure you're using the latest version of the mdshare library.
Check the download URL: Verify that the download URL is correct and not blocked by any firewall or proxy.

If the above troubleshooting steps don't resolve the issue, try the following solutions:

Use a different download method: Instead of using the mdshare library, try downloading the data manually from the website https://markovmodel.github.io/mdshare/pentapeptide/.
Use a different server: If the ftp.imp.fu-berlin.de server is not accessible, try using a different server that provides the same data.
Contact the data provider: Reach out to the data provider or the mdshare library maintainers to report the issue and ask for assistance.

The inability to download MD trajectory data can be frustrating, but there are often solutions available. By troubleshooting the issue, checking the server status, and using alternative download options, you can overcome the challenges and access the data you need. Remember to stay up-to-date with the latest mdshare library version and to contact the data provider or maintainers for assistance when needed.

For more information on the mdshare library and MD trajectory data, check out the following resources:

mdshare library documentation: https://mdshare.readthedocs.io/en/latest/
MD trajectory data: https://markovmodel.github.io/mdshare/
Down for Everyone or Just Me: https://downforeveryoneorjustme.com/
The md traj data cannot download now: Q&A

In our previous article, we explored the issue of md traj data not downloading, specifically focusing on the mdshare library and the ftp.imp.fu-berlin.de server. We provided troubleshooting steps and solutions to overcome these challenges. In this article, we'll answer some frequently asked questions (FAQs) related to the issue.

Q: What is the mdshare library?

A: The mdshare library is a Python package that provides a convenient way to download molecular dynamics (MD) trajectory data from various sources.

Q: Why is the ftp.imp.fu-berlin.de server not accessible?

A: The ftp.imp.fu-berlin.de server may be experiencing technical difficulties, or it may be blocked by your network or firewall. You can try checking the server status using online tools like Down for Everyone or Just Me.

Q: How do I troubleshoot the issue?

A: To troubleshoot the issue, follow these steps:

Check the server status.
Check the network connection.
Check the mdshare library version.
Check the download URL.

Q: What are some alternative download options?

A: You can try downloading the data manually from the website https://markovmodel.github.io/mdshare/pentapeptide/ or using a different server that provides the same data.

Q: How do I contact the data provider or maintainers?

A: You can reach out to the data provider or the mdshare library maintainers through their website or by sending an email to their support address.

Q: What are some common errors that occur when downloading MD trajectory data?

A: Some common errors that occur when downloading MD trajectory data include:

HTTPConnectionPool errors
NewConnectionError errors
No route to host errors
Connection timed out errors

Q: How do I resolve these errors?

A: To resolve these errors, try the following:

Check the server status.
Check the network connection.
Check the mdshare library version.
Check the download URL.
Try using a different download method or server.

Q: What are some best practices for downloading MD trajectory data?

A: Some best practices for downloading MD trajectory data include:

Checking the server status before downloading.
Using a stable network connection.
Checking the mdshare library version.
Checking the download URL.
Using a different download method or server if necessary.

The inability to download MD trajectory data can be frustrating, but there are often solutions available. By following the troubleshooting steps and using alternative download options, you can overcome the challenges and access the data you need. Remember to stay up-to-date with the latest mdshare library version and to contact the data provider or maintainers for assistance when needed.

For more information on the mdshare library and MD trajectory data, check out the following resources:

mdshare library documentation: https://mdshare.readthedocs.io/en/latest/
MD trajectory data: https://markovmodel.github.io/mdshare/
Down for Everyone or Just Me: https://downforeveryoneorjustme.com/