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4 votes

Nonbonded interactions on the GPU

As the error tells you: the GROMACS binary has been built without GPU support. Did you install gromacs with apt-get? Usually ...
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4 votes
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GROMACS Coordinates and velocity and force trajectories do not match accuracy

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” ...
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3 votes
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What are the units for the force output by nstfout, the velocity output by nstvout, and the coordinates output by nstxout in gromacs?

nstxout, nstvout and nstfout are the number of steps between coordinates, speed and forces ...
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2 votes
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GROMACS RMSF Result Analysis Problem

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 ...
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2 votes

How to make a video of a gromacs gmx dump standard output with VMD

No need to use gmx dump, you can simply load a xtc or trr trajectory in VMD using: ...
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2 votes
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gmx mdrun error: "Error in user input: 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 ...
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1 vote

gmx mdrun error: "Error in user input: Invalid input values In option s"

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 ...
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1 vote

Gromacs molecular dynamic simulation throwing error during minimization

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-...

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