[gmx-users] Center of my simulation box

Christopher Neale chris.neale at mail.utoronto.ca
Wed Oct 24 22:47:28 CEST 2012

No, that will not work because the offset will be different in different frames. What you want is trjconv -center
but you will need a modified trjconv program to so this so that you center based on the center of mass as outlined 
here: http://www.mail-archive.com/gmx-users@gromacs.org/msg41681.html

Then, you still have the problem that g_density builds the map up from min(z) toward max(z), so when max(z) - 
min(z) changes (as it does in a constant pressure simulation), then the center of your box is at a different position 
in each frame. 

I presume that your question was "how can I use g_density properly with any method other than the one already 
provided by Chris Neale". I personally have not seen anybody suggest a different method, but perhaps somebody 
else does have another method that they will share with you here.

I'm going to leave this thread now as I believe that it is going in circles. It is a tough problem, no doubt, but there
is already at least one complete solution available to you.


> Dear All users
> How can i change center of my simulation box to my considered
> coordinate in g_density program?
> -- 
> Sincerely
> Ali Alizadeh
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list