AMBER Archive (2004)

Subject: Re: AMBER: image and restart problems

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Jun 29 2004 - 09:57:42 CDT


the dimer separation could be fine, just because they are being
wrapped. Use ptraj to put things back together- center on 1
monomer, and do an image command. that should help.

  ----- Original Message -----
  From: Steve Seibold
  To: amber_at_scripps.edu
  Sent: Tuesday, June 29, 2004 8:56 AM
  Subject: AMBER: image and restart problems

  Hello

  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************ 864.3070980

  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

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