Probably "garbage in, garbage out." However you're measuring the density probably depends on share/top/atommass.dat, which relies on matching atom names to infer atom types and thus masses. If your atom names don't follow its assumptions... at least some tools warn about this in the output. Did the tool you were using not do so?
Mark On Tue, May 20, 2014 at 12:50 PM, sujithkakkat . <sujithk...@gmail.com>wrote: > Hello, > > I am working on a water-methane system with OPLSAA for methane and > TIP4P/Ice for water. > What I find strange is that after solvating the methane molecule with water > (tip4p/ice) using the genbox routine, the density appears to be very high > at 1661.04 (g/l) . The number of water molecules is normal for the box > size, and therefore should give lower density values. After equilibration > steps the density gets back to normal. > > Earlier , I ignored this problem and went ahead with the simulations, > and the end results were found to be good. For eg, the solvation free > energy of methane I calculated , was very close to reported values and also > the value obtained in Justin's tutorial. Another test was simulating the > tip4p/ice water , which gave results, for example the RDFs very close to > the reported results. > > Could some one comment what is going on that gives the high density? > > Regards, > > Sujith. > -- > 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.
