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" <nho...@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 > -- > 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. > -- 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.