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gmx mdrun error Invalid input values In option s"
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Meg Osterby
gmx mdrun error Invalid input values In option s"
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.
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.
, are you able to help us out at all with those? I'm trying to help take care of the unanswered queue.More
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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.
I think there was a misunderstanding here. Two errors are in user5520049's post.
A .tpr is not present in the workingdirectory so gromacs complains, if your .tpr is topol then you have to give this fileto 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.
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.tprMore
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
$PATHenvironmental 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
mdrunbinary. However, if themdrunwas 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
mdrunit 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.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
$PATHenvironmental 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
mdrunbinary. However, if themdrunwas 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
mdrunit 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.More
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I think there was a misunderstanding here. Two errors are in user5520049's post.
topolthen you have to give this file to gmx mdrun:gmx mdrun -s topol.gmx mdrun -h. That's why you had command not found and not because gmx is not in your $PATH. You couldn't have rungmx mdrunin the first place otherwise.Side tip: run
gmx mdrun -h -hiddento see hidden options.I think there was a misunderstanding here. Two errors are in user5520049's post.
topolthen you have to give this fileto gmx mdrun:gmx mdrun -s topol.gmx mdrun -h. That's why you had command not found and not because gmx is not in your $PATH. You couldn't have rungmx mdrunin the first place otherwise.Side tip: run
gmx mdrun -h -hiddento see hidden options.More
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