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.sewrote:
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.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-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
--
gmx-users mailing listgmx-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