AMBER Archive (2002)

Subject: iwrap and image

From: Sophia Kondratova (x357l_at_unb.ca)
Date: Wed Aug 28 2002 - 07:55:36 CDT

I am trying to do an MD simulation in a chloroform box. After doing a
minimization, the box looks normal (looking with the help of ptraj). When I
try to equilibrate with nvt ensemble, the box does not look square anymore
but with gaps and holes. The longer the simulation runs, the more missshaped
the box looks. The iwrap=1, and also I have used the image command of ptraj
(image center familiar). None of this changes the irregular shape of the box.
The same thing happens after an npt equilibration. Does this have anything to
do with the fact that I am trying to use chloroform?

Any help would be greatly appreciated.

Sophia Kondratova
Chemistry Department
University of New Brunswick
Canada