AMBER Archive (2001)

Subject: ptraj image for octahedral box

From: Peter Varnai (Peter.Varnai_at_ibpc.fr)
Date: Tue Mar 13 2001 - 09:47:28 CST

Dear Amber Users,

I am trying to postprocess a trajectory of a simulation
in a octahedral box to get the water molecules back to
the box around a DNA (atoms 1-762):

image center familiar com :1-762

The result is a discontinuous, fragmented water environment
around the DNA. Help on how to do this correctly with ptraj
(amber6) is welcome!

Thank you,
Peter Varnai