[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.

Groeten, David.
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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