[gmx-users] fluorine parameters in GROMACS
David van der Spoel
spoel at xray.bmc.uu.se
Tue Mar 19 12:46:23 CET 2002
On Mon, 18 Mar 2002, Erik Lindahl wrote:
>> The standard GROMACS force fields (ffgmxnb.itp) lists as
>> [ atomtypes ]
>> ;name mass charge ptype c6 c12
>> F 18.99840 0.000 A 0.78301E-02 0.25209E-04,
>> and GROMOS (ffG43b1nb.itp) lists as
>> F 0.000 0.000 A 0.0011778624 7.6073284e-07.
>> These c6 and c12 are largely different each other.
This is rather unfortunate, I don't know what the GROMOS variant is
based on, I only know that Van Buuren did some very low level quantum
chemistry (possibly semi empirical) to get charges for TFE. There was
actually another paper from De Loof (see tfe.itp) with different charges.
I don't know where the LJ parameters come from. Even if they come from
nowhere it should of course be possible to verify that they are not
complete nonsense by testing energies and densities of model compounds.
Finally, as we have 4 or 5 different C and O atomtypes, there probably has
to be more than one F as well.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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