[gmx-users] energy minimization and ions

Nuno R. L. Ferreira nunolf at ci.uc.pt
Wed Apr 28 15:08:01 CEST 2004

  ----- Original Message ----- 
  From: Ruben Martinez Buey 
  To: gmx-users at gromacs.org 
  Sent: Wednesday, April 28, 2004 1:47 PM
  Subject: [gmx-users] energy minimization and ions

  Hi all, 
  I want to energy minimize a structure (two proteins + 4 ligands) in a water box (dodecahedron). The total charge is not 0. what should I do better: 
  - add the ions I need to avoid this charge. 
  - add negative ions to compensate the positive charges (Asn, Gln in the protein and positive charges in the ligands) and positive ions to compensate negative charges (Glu, Asp in the protein and ligands), so the total charge will be 0. 

  Just neutralize the system. The two options that you posed seem to me are the same, arent't they?



  Thanks in advance, 

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