image command of ptraj

From: Xiaolin Chuang <>
Date: Wed 17 Oct 2001 12:22:20 +0000

Dear Experts,

As I have known, image command of program PTRAJ makes all molecules to be in
the box leading to a good visual of simulation box and there is no effect
with any energy. However, I have extracted WAT residues around DNA within 5
Angstrom from original trajectory and from trajectory performed image
command. I found that the number of water molecules obtained from the both
trajectory files are different. This means that if I want to do anything
with WAT residues, I should use original trajectory file, right?

By the way, if I run MD with iwrap=0 or iwrap=1, I should obtain the
difference structure of solvent. Is it true?

Any suggestion is appreciated.

Many thanks in advance.


Get your FREE download of MSN Explorer at

Received on Wed Oct 17 2001 - 05:22:20 PDT
Custom Search