AMBER Archive (2008)

Subject: AMBER: ptraj problem with centering in the box

From: Hannes Wallnoefer (
Date: Wed Jul 02 2008 - 09:00:33 CDT

Hello Amber-users,

I have a problem when i want to get my protein back into the box after the MD. I
tried the following ptraj script:

trajin trajectory files
center origin :1-234
image origin center
trajout output trajectory

1-234 are the residues of my protein.
When i look at the output trajectory there is a gap in the box. This gap moves
during the trajectory. It seems as if there is a small slide of vacuum between
all of the periodic boxes. I added a screenshot of the last snapshot.
Has anybody ever seen that? Are there suggestions how to get rid of that or what
has gone wrong?

Best regards,

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