AMBER Archive (2008)

Subject: AMBER: Dimension of the solvated box?

From: abiram abiram (mail2abiram_at_yahoo.co.in)
Date: Wed Feb 20 2008 - 07:54:08 CST

Dear Amber Users,
   
       I was trying to save the top and crd files for the peptide solvated in TIP3 water model. I have few questions regarding the dimension of the box constructed while solvating the peptide..
   
  Below i have pasted the box information appeared during solvation..
   
  ---------------------------------------
  Force field used : ff03
   
  Solvated with 10.0A cutoff
   
  Solute vdw bounding box: 16.500 16.880 6.410
   
  Total bounding box for atom centers: 36.500 36.880 26.410
   
  Solvent unit box : 18.774 18.774 18.774
   
  Total vdw box size :39.546 40.343 29.587A
   
  volume: 47203.563A
   
  Total mass 18724.810amu Density 0.659g/cc
   
  Added 1009 residues
   
  ----------------------------------------
   
  1) Can somebody tell me which of the line in the above gives the dimension of the box.
   
  2) I want to know, whether that dimension is considered as the unit cell boxlengths for PBC simulations.
   
  3) Also why there is a large difference in the thrid parameter of the lines indicating "Solute vdw bounding box, Total bounding box for atom centers, Solvent unit box, Total vdw box size ".
   
  Kindly help.
   
  Thanks in advance
   
  A. Abiram
   
     

       
---------------------------------
 Save all your chat conversations. Find them online.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu