Here you ask and answer questions on GROMACS , a free and open-source software suite for high-performance molecular dynamics and output analysis.

• User discussions: Discussion forum for installation and usage of GROMACS software. To post a new topic or to answer to a topic, an account is required.
• Announcements: GROMACS-related announcements. Only staff can post.
• Developers discussions: Discussion forum on GROMACS development and related software. Here you can discuss your ideas and intentions related to the development of GROMACS. Interested in participating, please click here to send a request to join the GROMACS developers group.
• GROMACS polls: here you can provide your input on GROMACS-related topic or initiative by answering to posted polls.(About the GROMACS polls category)
• Third party tools and files: here you can find or you can announce third party tools and files useful for the GROMACS community
• Site feedback for any questions about how things work on this site
• Open position announcements: here you can post about open positions in the field of molecular dynamics simulations and/or of interest of the GROMACS community. The category is moderated. Note that the contents are not necessarily verified or endorsed by the GROMACS team.

Some tips to improve the chance of getting helpful response

Some tips to improve the chance of getting helpful response to your problem:

1. Use an informative title for your topic and use one topic for each individual question;
2. Provide as much detailed information as possible on the problem. For example when you post in user discussions:

• say why you thought the output was not what you expected, (this should be higher up in my opinion)
• cite your GROMACS version number and specify if the code has been modified,
• describe your simulation system (e.g. system type, size, box type, force field),
• describe your simulation preparation before the problem arose (e.g. manual modification of files),
• copy and paste your input command lines,
• consider including your .mdp file or the relevant portion of your .top or .log file,
• consider uploading a relevant image or PDF,
• inspect all your output files, stderr and stdout for information,
• copy and paste any error message (look in both the .log file and stderr);

3. When you’ve solved the problem, please consider posting a reply to the forum detailing what was wrong, your solution and how it worked. Not only might this help people in the future, but it might teach you more about the problem and the solution;
4. use good etiquette, avoiding ALL CAPS, avoiding expressions like “urgent” or “help” in the title, bad spelling and punctuation, txtspk, perso. abbrs, etc
5. Use tags. Here you find more on how to use Forum tags

Useful information, once you have created an account

• Set your account preference by clicking your name at the top-right side. In particular:
  to activate mailing-list mode go to preference > email
  to change the appearance of your profile go to preference > interface
• To post via email to user discussion use bioexcel1+gromacs-user-forum@discoursemail.com.
  Note, to post via email, it is important that you subscribe with the mail address exactly as it appears in the headers of the mails you send, otherwise your posts will be rejected! ( E.g. joe@chem.uni.edu is different from joe@uni.edu; and joe.doe@gmail.com is different from joedoe@gmail.com. )

Note the complete list of the accounts is available only to the forum administrators.

You find our admins and forum contact info at the about GROMACS forums page.

This is a Civilized Place for Public Discussion

Please treat this discussion forum with the same respect you would a public park. We, too, are a shared community resource — a place to share skills, knowledge and interests through ongoing conversation.

These are not hard and fast rules, merely guidelines to aid the human judgment of our community and keep this a clean and well-lighted place for civilized public discourse.

Improve the Discussion

Help us make this a great place for discussion by always working to improve the discussion in some way, however small. If you are not sure your post adds to the conversation, think over what you want to say and try again later.

The topics discussed here matter to us, and we want you to act as if they matter to you, too. Be respectful of the topics and the people discussing them, even if you disagree with some of what is being said.

One way to improve the discussion is by discovering ones that are already happening. Spend time browsing the topics here before replying or starting your own, and you’ll have a better chance of meeting others who share your interests.

Be Agreeable, Even When You Disagree

You may wish to respond to something by disagreeing with it. That’s fine. But remember to criticize ideas, not people. Please avoid:

• Name-calling
• Ad hominem attacks
• Responding to a post’s tone instead of its actual content
• Knee-jerk contradiction

Instead, provide reasoned counter-arguments that improve the conversation.

Your Participation Counts

The conversations we have here set the tone for every new arrival. Help us influence the future of this community by choosing to engage in discussions that make this forum an interesting place to be — and avoiding those that do not.

Discourse provides tools that enable the community to collectively identify the best (and worst) contributions: bookmarks, likes, flags, replies, edits, and so forth. Use these tools to improve your own experience, and everyone else’s, too.

Let’s leave our community better than we found it.

If You See a Problem, Flag It

Moderators have special authority; they are responsible for this forum. But so are you. With your help, moderators can be community facilitators, not just janitors or police.

When you see bad behavior, don’t reply. It encourages the bad behavior by acknowledging it, consumes your energy, and wastes everyone’s time. Just flag it. If enough flags accrue, action will be taken, either automatically or by moderator intervention.

In order to maintain our community, moderators reserve the right to remove any content and any user account for any reason at any time. Moderators do not preview new posts; the moderators and site operators take no responsibility for any content posted by the community.
See here how-to-do it

Always Be Civil

Nothing sabotages a healthy conversation like rudeness:

• Be civil. Don’t post anything that a reasonable person would consider offensive, abusive, or hate speech.
• Keep it clean. Don’t post anything obscene or sexually explicit.
• Respect each other. Don’t harass or grief anyone, impersonate people, or expose their private information.
• Respect our forum. Don’t post spam or otherwise vandalize the forum.

These are not concrete terms with precise definitions — avoid even the appearance of any of these things. If you’re unsure, ask yourself how you would feel if your post was featured on the front page of the New York Times.

This is a public forum, and search engines index these discussions. Keep the language, links, and images safe for family and friends.

Keep It Tidy

Make the effort to put things in the right place, so that we can spend more time discussing and less cleaning up. So:

• Don’t start a topic in the wrong category.
• Don’t cross-post the same thing in multiple topics.
• Don’t post no-content replies.
• Don’t divert a topic by changing it midstream.
• Don’t sign your posts — every post has your profile information attached to it.

Rather than posting “+1” or “Agreed”, use the Like button. Rather than taking an existing topic in a radically different direction, use Reply as a Linked Topic.

Post Only Your Own Stuff

You may not post anything digital that belongs to someone else without permission. You may not post descriptions of, links to, or methods for stealing someone’s intellectual property (software, video, audio, images), or for breaking any other law.

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This site is operated by your friendly local staff and you, the community. If you have any further questions about how things should work here, open a new topic in the site feedback category and let’s discuss! If there’s a critical or urgent issue that can’t be handled by a meta topic or flag, contact us via forum-master email.

Terms of Service

Yes, legalese is boring, but we must protect ourselves – and by extension, you and your data – against unfriendly folks. We have a Terms of Service describing your (and our) behavior and rights related to content, privacy, and laws. To use this service, you must agree to abide by our TOS.