In addition to that information, what parameters are you using for O2? It
sounds like something is super attractive within your system, causing the O2 to
condense. At what temperature are you simulating?
-Justin
Vitaly Chaban wrote:
Could you provide a movie or at least snapshots? What about energy of
the system? How it changes?
Sorry I am not very good at describing my system. After running the
simulation for a while or equilibrating the system all the oxygen
molecules move along one wall (a rectangular box with the long side in
the z direction and the shorter sides in the x and y direction at the
origin) of my periodic boundary condition box. The nitrogen molecules
stay fairly evenly distributed in the simulation box. I checked all the
parameters and the charges were set to 0. I have about 175.2 g/l
nitrogen and 56.5 g/l oxygen in my system. I realize this is higher
pressure than atmosphere and have purposely done this.
Andy
On Tue, Aug 26, 2008 at 5:28 AM, Vitaly Chaban <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Using the parameters listed earlier I equalized my system after trying to
place the oxygen and nitrogen molecules evenly throughout my system. The
result showed the nitrogen molecules fairly even throughout the system but
all the oxygen molecules on one side. Any ideas on why the system
might not
be equalizing out to an even distribution of oxygen by nitrogen?
What's the density of O2 and N2 in your system?
What's "all the oxygen molecules on one side"? What side?
Are you sure no occasional charges are present on some site in your
system?
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
skype: vvchaban
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
skype: vvchaban
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
