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

[Tsjerk Wassenaar]

Hi Nathan,

Yes, placement of molecules neglects the interactions. You need to simulate
the stuff before drawing conclusions.

Cheers,

Tsjerk
On Mar 31, 2015 8:43 AM, "Nathan K Houtz" <nhoutz at purdue.edu> wrote:

> 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
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