[gmx-users] Re[2]: Using Morse potentials with ENCAD force field

[Justin A. Lemkul]

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 <chaban at univer.kharkov.ua 
> <mailto:chaban at univer.kharkov.ua>> 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: chaban at univer.kharkov.ua <mailto:chaban at univer.kharkov.ua>
> 
> skype: vvchaban
> 
> 
> 
> 
> 
> 
> -- 
> 
> Vitaly V. Chaban
> 
> School of Chemistry
> 
> National University of Kharkiv
> 
> Svoboda sq.,4, Kharkiv 61077, Ukraine
> 
> email: chaban at univer.kharkov.ua <mailto:chaban at univer.kharkov.ua>
> 
> skype: vvchaban
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> 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

========================================