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Dear GROMACS users,
I have been trying to equilibrate 240 molecules of toluene in a simulation box with dimensions 3.3 x 3.3 x 3.9 nm. After 160 ns of NPT equilibration, I did not achieve the target average pressure of 1 bar (the measured pressure was -0.173205 bar), and the averaged density was 953.738 kg/m³, whereas the actual density of toluene is 867 kg/m³.
In an attempt to resolve this, I repeated the procedure with a reduced number of toluene molecules, but the density still could not be optimized. I also tried using the united atom model, but the average density remained high at 949 kg/m³.
I am attaching a link to the box details, as well as the npt.mdp
and npt.log
files for both all-atom and united atom models of toluene. I would appreciate any guidance on how to resolve this issue and achieve the correct density.
Thank you for your assistance.