[gmx-users] Center of my simulation box
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
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?
> Ali Alizadeh
> gmx-users mailing list gmx-users at gromacs.org
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