text: user7248: I'm new to bioinformatics and gromacs 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
  
  
  user9109: I think there was a misunderstanding here. Two errors are in user5520049's post.
  
  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.
  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.
  
  user57: 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 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 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.
  
original_text: 7248: <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>
   9109: <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 $PATH. You couldn't have run <code>gmx mdrun</code> in the first place otherwise.</li>
  </ol>
  <p>Side tip: run <code>gmx mdrun -h -hidden</code> to see hidden options.</p>
   57: <p>If the command line says &quot;command not found&quot;, it means that the binary is not executable or not found in any of the paths mentioned in the <code>$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>
  