Thank you Mark, My Bad. Now fixed.
Hope the simulations I did before were not affected, I had defined atomtypes with the correct mass in the .itp file used. Sujith On Wed, May 21, 2014 at 12:59 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > 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. > -- 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.