Gmx density error

User discussions
1

GROMACS version:2024.1
GROMACS modification: Yes/No

Dear All, I have 1us simulation of an ion channels embded in lipid bilayer. I am trying the calculate the density of different components as per the command below-
$ gmx density -f outputbox.xtc -s step6.1_equilibration.tpr -o density_popcX.xvg -d X
i am able to calculate density for Ca ions. However, when i am calculating density for lipids or other components, the program hangs. Am i doing anything wrong?

Thank you
Veeru

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2

Have you checked that the .xtc file looks OK, in e.g., VMD? Has it been processed after the simulations? Was the whole system written to the .xtc file?

The tool shouldn’t hang anyhow, but it would be good to try to narrow down what might be the issue.