AMBER Archive (2004)

Subject: AMBER: image and restart problems

From: Steve Seibold (
Date: Tue Jun 29 2004 - 07:56:52 CDT


I am running a long (5-20 ns) MD simulation with a homodimer with
explicit waters. After about 4 ns I noticed that my restart files were
corrupted. The coordinates in them were replaced with "********" in many
places: as shown below:

18273 0.1137100E+05

-458.5618828************ 865.8784605-458.1478773************
865.9780753- 459.5624384************ 865.9971669-458.3306444************
864.5385748- 459.1445772************ 863.8556527-457.4029599************

Thinking that the problem might be that this was an image problem with
the water molecules, I started using "iwrap=1" to wrap the waters back
into the box. However, after running for 500 ps or so now my homodimer
has separated from each other AND translated out of the water box.

Can some one please give me some help?

I am attaching my input file.

Thanks, Steve


  • application/octet-stream attachment:
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