Density of toluene is not getting equilibrated during NPT equilibration

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1

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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.

2

Which forcefield are you using? Also, how did you get the 240 molecules? Does the value translate to 953 kg/m3 for a simulation box with dimensions 3.3 x 3.3 x 3.9 nm?

3

what is the compressiblity you used? the files are not accessbile

4

Dear @scinikhil,

Thank you for your response. I apologize for the mistake in my previous message. The files are now accessible.

Regarding your question about the compressibility used, I used a compressibility value of 4.5e-5.

Thank you for your understanding.

5

Dear @Teslim, Thank you for your reply. I have used Gromos 54a7 forcefield. The number of molecules I have calculated from the density of the molecule (867 kg/m3)and volume of box 3.3x3.3x3.9 nm3