[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
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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