[gmx-users] Charge calcn
feenstra at chem.vu.nl
Mon Mar 1 15:11:01 CET 2004
Mungikar, Amol Arvind (UMR-Student) wrote:
> 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:
> ASPARTIC ACID
> 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.
Charges are not calculated, they are part of the forcefield parameters
and are set in the respective .rtp files.
IMHO, vacuum calculations are pretty useless. If you must do it for some
reason, you should probably use the Gromos Vacuum (43b1) forcefield.
The Gromacs forcefield is badly outdated, is deprecated, and should not be
used anymore. It was never developed for any type of vacuum calculation.
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