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As the error tells you: the GROMACS binary has been built without GPU support. Did you install gromacs with apt-get? Usually these kind of programs are shipped with a basic built, with a lot of features disabled. If you did built gromacs from source, then cuda was not found during configuration. I would try building gromacs from source and: be sure cuda is ...


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From GROMACS documentation about reproducibility: The following factors affect the reproducibility of a simulation, and thus its output: Precision (mixed / double) with double giving “better” reproducibility. Number of cores, due to different order in which forces are accumulated. For instance (a+b)+c is not necessarily binary identical to a+(b+c) in ...


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nstxout, nstvout and nstfout are the number of steps between coordinates, speed and forces written in the output trajectory (Output control documentation). As for the units present in your trajectory files (say a .trr): coordinates are in nm, speeds in nm.μs⁻¹ (so in mm.m⁻¹) and forces in kJ.mol⁻¹.nm⁻¹. These should be consistent through all GROMACS files (...


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The residue numbering in a PDB file mainly depend on the person who deposited it. There are usually reasons for how things are numbered, but ultimately you should look at PDB file, and check the details on how the structure was obtained. To give you an example, during my PhD I worked on a protein that had some missing residues at the N-terminus. That was ...


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No need to use gmx dump, you can simply load a xtc or trr trajectory in VMD using: vmd path/to/gro_file.gro other/path/to/trajectory_file.xtc As always you can also use the GUI to first open your gro file, then right click on the molecule and select Load data into molecule before selecting your xtc or trr file. After putting the representations as you see ...


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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 ...


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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 ...


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Answer from @user1271772, converted from comment: Try on this site: https://mattermodeling.stackexchange.com/questions/tagged/gromacs. There's an entire GROMACS tag there. Answer from @vishal-kumar-sahu, converted from comment: Try running/resuming using -cpi the simulation again, I got NaN error and rerun kept continued.


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