I am concerned about the number density of water. At T = 300 K and P = 1 atm, SPC/E water has certain number density (no. of molecules/nm^3). With genbox I get .gro file with 34.04 molecules/nm^3 number density, which will remain constant even if I do equilibration in NVT simulation set up. So does that 34.04 molecules/nm^3 corresponds to thermodynamic condition of water at 300K and 1 atm.
thanks sikandar On Fri, Jun 18, 2010 at 12:20 PM, David van der Spoel <sp...@xray.bmc.uu.se>wrote: > On 2010-06-18 18.24, Sikandar Mashayak wrote: > >> Hi >> >> When a bulk SPC/E water box(.gro) is created using the command "genbox >> -cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic condition of >> water? >> >> Is it 300K at 1atm? >> >> thanks >> sikandar >> >> No. You have to equilibrate because the box is not completely full. > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > 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/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/mailing_lists/users.php >
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