[gmx-users] Charge calcn

Mungikar, Amol Arvind (UMR-Student) mungikar at umr.edu
Thu Feb 26 18:22:01 CET 2004

Dear gromacs users,
I have few basic questions regarding type of force field to be used for vacuum simulation and charges involved therein:
1. For vacuum simulation can the GROMACS force field (option '0' in 'pdb2gmx' command) be used?, instead of GRO96 43b1 (option '3' in pdb2gmx)- vacuum force field?
2. How the charges are calculated in both the cases, to be specific: 
    e.g; If I have:
         Side Chain: COO-; with atom types C (bare carbon) & OM(carboxyl oxyegn)
Then both the force field mentioned above give different charges on this side chains. GROMACS gives me -1 charge on the COO- side chain, while GRO9643b1 gives me a net charge of zero on COO-? I would appreciate if somebody can help me understand this.
Thank you very much in advance.

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