Nathan, The experimental data ideally corresponds to an infinitely long, well-converged MD simulation at the corresponding set of temperature and pressure, not after EM and most certainly not after just filling a box, where spacing is according to a preset cut-off and not due to interatomic interactions.
Alex NKH> Hello Gromacs users, NKH> I tried to create a 6.5 nm cubic box of tetrolic acid (otherwise NKH> known as 2-butynoic acid), but the density is too low. According NKH> to this, http://www.chemspider.com/Chemical-Structure.61810.html, NKH> the density should be about 0.964 NKH> g/mL. Given the molecular weight of tetrolic acid, this NKH> corresponds to right around 1900 molecules in the 6.5 nm box I NKH> prepared. Unfortunately, when I attempted to fill the box, NKH> Gromacs only found room for 1676 molecules, resulting in NKH> a density of 0.852 g/mL. I know that models are not 100% NKH> accurate, but I'm worried about a difference that big. Should I NKH> expect the system to condense when I minimize, and just shrink NKH> the box afterwards? Or do you think there is NKH> another problem? NKH> Thanks for your help, NKH> Nathan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
