Hi, editconf needs to take the masses from a database file if not fed with a run input file. It will probably miss out on some types of atoms or get the masses wrong, especially with united atoms and/or dummies. Probably the density would be correct giving a .tpr file for input.
Cheers, Tsjerk On Mon, Jan 10, 2011 at 4:06 PM, <ka...@rishi.serc.iisc.ernet.in> wrote: > > > Sir, > > I am using Gromacs 4.0.7 version. Does this problem exits > in other older or newer versions? what is the density of water > that spc216 adds? If it is a fixed density, then i encountered > a problem - > > > I tried using 1 water molecule as a system (instead of protein), in a > cubic box with 0.8nm distance (-d), and filled it with spc216 water, > in this case the density it showed was 933.221g/l, > > -------------------------------------------------------------------- > Output configuration contains 513 atoms in 171 residues > Volume : 5.48157 (nm^3) > Density : 933.221 (g/l) > Number of SOL molecules: 171 > --------------------------------------------------------------------- > > but when I used the same system i.e water, with a cubic box of 1.0nm > distact from water (-d) and filled with spc216 water it gave a density > of 1001.85g/l, > > ---------------------------------------------------------------------- > Output configuration contains 1017 atoms in 339 residues > Volume : 10.1226 (nm^3) > Density : 1001.85 (g/l) > Number of SOL molecules: 339 > ---------------------------------------------------------------------- > > So does this trend indicate that the density increases with increase in > volume of the same system? and spc216 does not add water according to > a specific density? > > With Regards > MKS > >> Hmm, that's the second post in a week reporting editconf giving an >> apparently spurious measurement of the mass. Sounds like it could be a >> bug. Thoughts, anyone? >> >> Mark >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
