Answers.Body: <p>I think there was a misunderstanding here. Two errors are in user5520049's post.</p>
  <ol>
  <li>A .tpr is not present in the working
  directory so gromacs complains, if your .tpr is <code>topol</code> then you have to give this file
  to <strong>gmx mdrun</strong>:  <code>gmx mdrun -s topol</code>.</li>
  <li>mdrun is not a command, you should have called instead: <code>gmx mdrun -h</code>. That's why you had command not found and not because gmx is not in your $PATH. You couldn't have run <code>gmx mdrun</code> in the first place otherwise.</li>
  </ol>
  <p>Side tip: run <code>gmx mdrun -h -hidden</code> to see hidden options.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-02T21:04:28.400Z
Answers.Text: thanks for helping . the path is also was a problem but your answer is important for me . i tried to execute those commands gmx grompp -f run_$count.mdp -p topol.top -c em.gro -o run_$count.tpr -nb gpu;
  gmx mdrun -deffnm run_$count -nb gpu and got the same error although topol.tpr is exists in the directory
Answers.UserDisplayName: user5520049
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-03T16:01:47.407Z
Answers.Text: I can assure you that gmx is in your $PATH, you could not launch any gmx commands otherwise (gmx grompp or mdrun etc.).
  The problem is that you use **-deffnm** (which you didn't mention in your orginal post btw) with gmx mdrun which is the option to setup default input and output names. So with **-deffnm un_count** gromacs is looking for a tpr named: un_count.tpr and not topol.tpr. Either:
  1. use **-deffnm un_count** and name your tpr un_count.tpr
  2. do not use -deffnm and not use -s and have default topol.tpr in the working directory.
  3. do not use -deffnm & use -s yourcustomtpr.tpr
Answers.UserDisplayName: jeremy
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-03T16:17:31.467Z
Answers.Text: Here is a link to good gromacs tutorials: http://www.mdtutorials.com/gmx/ , maybe you could take a look to be familiarized with this MD engine ;)
Answers.UserDisplayName: jeremy
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-17T18:56:32.497Z
Answers.Text: This was a great answer Jeremy! We have a [few unanswered GROMACS questions here](https://mattermodeling.stackexchange.com/questions/tagged/gromacs?tab=Unanswered), are you able to help us out at all with those? I'm trying to help take care of the unanswered queue.
Answers.UserDisplayName: user1271772
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-02T10:46:36.677Z
Answers.LastActivityDate: 2020-11-02T11:07:02.127Z
Answers.LastEditDate: 2020-11-02T11:07:02.127Z
Answers.UserDisplayName: jeremy
Answers.Body: <p>If the command line says &quot;command not found&quot;, it means that the binary is not executable or not found in any of the paths mentioned in the <code>$PATH</code> environmental variable. You can check for example <a href="https://www.cyberciti.biz/faq/linux-unix-command-not-found-error-and-how-to-get-rid-of-it/" rel="nofollow noreferrer">this tutorial</a> for details on how it works and how to resolve problems related to this variable.</p>
  <p>Which probably means, that you need to go a step back, to <a href="http://manual.gromacs.org/documentation/current/install-guide/index.html#building-just-the-mdrun-binary" rel="nofollow noreferrer">the installation instructions of gromacs</a> and try to install the <code>mdrun</code> binary. However, if the <code>mdrun</code> was not installed successfully, it's very likely that more stuff of the package will be missing, so it might be worth reinstalling it all.</p>
  <p>P.S. It's not obvious to me if getting <code>mdrun</code> it will resolve the first posted problem (I have never worked with gromacs). If you would share the link to the research you have done, that would help others to help you.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-17T18:56:51.767Z
Answers.Text: This was a great answer Kamil! We have a [few unanswered GROMACS questions here](https://mattermodeling.stackexchange.com/questions/tagged/gromacs?tab=Unanswered), are you able to help us out at all with those? I'm trying to help take care of the unanswered queue.
Answers.UserDisplayName: user1271772
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-31T14:49:17.837Z
Answers.LastActivityDate: 2020-10-31T14:49:17.837Z
Answers.UserDisplayName: Kamil S Jaron
Body: <p>I'm new to bioinformatics and <a href="http://www.gromacs.org/" rel="nofollow noreferrer">gromacs</a> I tried to run the code and got this error</p>
  <pre><code>Program:     gmx mdrun, version 2020
  Source file: src/gromacs/options/options.cpp (line 179)
  Function:    void gmx::internal::OptionSectionImpl::finish()
  
  Error in user input:
  Invalid input values
  In option s
  Required option was not provided, and the default file 'topol' does not
  exist or is not accessible.
  The following extensions were tried to complete the file name:
    .tpr
  </code></pre>
  <p>I already have the file <code>topol</code>. I searched and found that I need to run <code>mdrun-h</code> to ensure that the command work but when I check</p>
  <pre><code>mdrun -h 
  </code></pre>
  <p>I got</p>
  <pre><code>mdrun: command not found
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-31T03:57:12.223Z
Comments.Text: try 'which mdrun', it might not simply be installed
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-31T04:27:37.720Z
Comments.Text: thanks for replying, I tried it and got nothing
Comments.UserDisplayName: user5520049
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-31T10:02:37.100Z
Comments.Text: @ATpoint has a good point! The problem is your environment is wrongly configured
Comments.UserDisplayName: M__
Tags: <gromacs>
Title: gmx mdrun error: "Error in user input: Invalid input values In option s"
ThreadText: # gmx mdrun error: "Error in user input: Invalid input values In option s"
  
  (Asked by: username_0 on 2020-10-31)
  
  I'm new to bioinformatics and [gromacs](http://www.gromacs.org/) I tried to run the code and got this error
  
  ```
  Program:     gmx mdrun, version 2020
  Source file: src/gromacs/options/options.cpp (line 179)
  Function:    void gmx::internal::OptionSectionImpl::finish()
  
  Error in user input:
  Invalid input values
  In option s
  Required option was not provided, and the default file 'topol' does not
  exist or is not accessible.
  The following extensions were tried to complete the file name:
    .tpr
  
  ```
  
  I already have the file `topol`. I searched and found that I need to run `mdrun-h` to ensure that the command work but when I check
  
  ```
  mdrun -h 
  
  ```
  
  I got
  
  ```
  mdrun: command not found
  
  ```
  
  **Tags:** gromacs
  
  > **Comments:**
  > **username_1**: try 'which mdrun', it might not simply be installed  
  > **username_0**: thanks for replying, I tried it and got nothing  
  > **username_1**: @ATpoint has a good point! The problem is your environment is wrongly configured  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_4 on 2020-10-31. Score: 2 | Accepted answer
  
  If the command line says "command not found", it means that the binary is not executable or not found in any of the paths mentioned in the `$PATH` environmental variable. You can check for example [this tutorial](https://www.cyberciti.biz/faq/linux-unix-command-not-found-error-and-how-to-get-rid-of-it/) for details on how it works and how to resolve problems related to this variable.
  
  Which probably means, that you need to go a step back, to [the installation instructions of gromacs](http://manual.gromacs.org/documentation/current/install-guide/index.html#building-just-the-mdrun-binary) and try to install the `mdrun` binary. However, if the `mdrun` was not installed successfully, it's very likely that more stuff of the package will be missing, so it might be worth reinstalling it all.
  
  P.S. It's not obvious to me if getting `mdrun` it will resolve the first posted problem (I have never worked with gromacs). If you would share the link to the research you have done, that would help others to help you.
  
  > **Comments:**
  > **username_3**: This was a great answer username_4! We have a [few unanswered GROMACS questions here](https://mattermodeling.stackexchange.com/questions/tagged/gromacs?tab=Unanswered), are you able to help us out at all with those? I'm trying to help take care of the unanswered queue.  
  
  ---
  
  ### Answer by username_2 on 2020-11-02. Score: 1
  
  I think there was a misunderstanding here. Two errors are in username_0's post.
  
  1. A .tpr is not present in the working
     directory so gromacs complains, if your .tpr is `topol` then you have to give this file
     to **gmx mdrun**: `gmx mdrun -s topol`.
  2. mdrun is not a command, you should have called instead: `gmx mdrun -h`. That's why you had command not found and not because gmx is not in your $PATH. You couldn't have run `gmx mdrun` in the first place otherwise.
  
  Side tip: run `gmx mdrun -h -hidden` to see hidden options.
  
  > **Comments:**
  > **username_0**: thanks for helping . the path is also was a problem but your answer is important for me . i tried to execute those commands gmx grompp -f run_$count.mdp -p topol.top -c em.gro -o run_$count.tpr -nb gpu; gmx mdrun -deffnm run_$count -nb gpu and got the same error although topol.tpr is exists in the directory  
  > **username_2**: I can assure you that gmx is in your $PATH, you could not launch any gmx commands otherwise (gmx grompp or mdrun etc.). The problem is that you use **-deffnm** (which you didn't mention in your orginal post btw) with gmx mdrun which is the option to setup default input and output names. So with **-deffnm un_count** gromacs is looking for a tpr named: un_count.tpr and not topol.tpr. Either: 1. use **-deffnm un_count** and name your tpr un_count.tpr 2. do not use -deffnm and not use -s and have default topol.tpr in the working directory. 3. do not use -deffnm & use -s yourcustomtpr.tpr  
  > **username_2**: Here is a link to good gromacs tutorials: http://www.mdtutorials.com/gmx/ , maybe you could take a look to be familiarized with this MD engine ;)  
  > **username_3**: This was a great answer username_2! We have a [few unanswered GROMACS questions here](https://mattermodeling.stackexchange.com/questions/tagged/gromacs?tab=Unanswered), are you able to help us out at all with those? I'm trying to help take care of the unanswered queue.  
  
  ---
  
  