[gmx-users] Vacuum Simulation

Joanne Hanna J.F.Hanna at warwick.ac.uk
Tue May 17 15:02:08 CEST 2005


I am trying to simulate my system in vacuum, i have run my protein and one of my ligands (a single phenylalanine) through pdb2gmx and selected the correct forcefield, however i am unsure of how to treat the charges for my other ligand AMP(2-) and the ion present Mg(2+). is it sufficient to allow these to balance each other out, or should each individual molecule carry a zero charge.

Many thanks

Joanne Hanna
Department of Chemistry
University of Warwick

J.F.Hanna at warwick.ac.uk
jfhanna at gmail.com

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