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