[gmx-users] Density of pure tetrolic acid does not agree with experimental data

[Nathan K Houtz]

Hello Gromacs users,

I tried to create a 6.5 nm cubic box of tetrolic acid (otherwise known as 2-butynoic acid), but the density is too low. According to this, http://www.chemspider.com/Chemical-Structure.61810.html, the density should be about 0.964 g/mL. Given the molecular weight of tetrolic acid, this corresponds to right around 1900 molecules in the 6.5 nm box I prepared. Unfortunately, when I attempted to fill the box, Gromacs only found room for 1676 molecules, resulting in a density of 0.852 g/mL. I know that models are not 100% accurate, but I'm worried about a difference that big. Should I expect the system to condense when I minimize, and just shrink the box afterwards? Or do you think there is another problem?

Thanks for your help,
Nathan