[gmx-users] genion

Nancy Deng jdeng at adrik.bchs.uh.edu
Wed Mar 2 01:58:22 CET 2005

I tried again with the -random option. Seems to me the problem fixed. The newly added ion is pretty far from the protein and it is near the face of the water box. Since I use "pbc" in my later simulation, so it looks fine.


  ----- Original Message ----- 
  From: Dallas Warren 
  To: Discussion list for GROMACS users 
  Sent: Tuesday, March 01, 2005 1:50 PM
  Subject: Re: [gmx-users] genion

    Probably genion placed solvent inside the protein, and you used genion without the -random option. In that case it places the ion where the potential is most favorable, which will usually be inside the protein.

  Has that been fixed?  I haven't tried to use the option for awhile now, as last time I did that was broken and it simply placed all ions along one face of the box.

  Catch ya,

  Dr. Dallas Warren
  Department of Pharmaceutical Biology and Pharmacology
  Victorian College of Pharmacy, Monash University
  381 Royal Parade, Parkville VIC 3010
  dallas.warren at vcp.monash.edu.au
  +61 3 9903 9083
  When the only tool you own is a hammer, every problem begins to resemble a nail. 


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