[gmx-users] periodic boundary conditions

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Thu Dec 4 17:56:01 CET 2003

I think the current version of gromacs has a bug in it. Download the CVS
beta version
I believe it has been fixed.


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of xiaoyi li
Sent: Thursday, December 04, 2003 6:46 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] periodic boundary conditions

Hi all,

I use periodic boundary conditions in my simulations by Gromacs. It said
in the manual that only one - the nearest image of each particle is
considered for short-range non-bonded interaction terms during the
simulations (called minimum image convention).

However, when i try to analysize the trajectory and calculate the
distance between two planes by g_sgangle, I found that the results
aren't got from the nearest image but the images in one cell. So the
results cannot be used directly whenever particles are near the

My question is: When we calculate the total energy by g_energy, is the
result got from images in one cell? If so, are there any method to get
the total energy and the distance from the nearest images?

Thanks in advance!

Uppsala University

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