[gmx-users] errors in ffG43a2nb.itp

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 29 13:08:58 CET 2001

On Thu, 29 Nov 2001, Marcos Villarreal wrote:

>Hello ,
>I have noticed some errors in ffG43a2nb.itp as well as in ffG43a1nb.itp and
>The most obvious is that  while atom type NR have a bigger c12 param than the
>others Nx atoms, the [ nonbond_params ] lines are the same
>       C       NT  1  0.0023880368  2.389937e-06
>       C       NL  1  0.0023880368  2.389937e-06
>       C       NR  1  0.0023880368  2.389937e-06
>     CH2       NT  1  0.0041605544  6.605177e-06
>     CH2       NL  1  0.0041605544  6.605177e-06
>     CH2       NR  1  0.0041605544  6.605177e-06
I'm not sure that is an error. The gromos96 force field is not purely
based on combination rules. E.g. the interaction between charged groups
(carboxylate with NH3+ or so) has larger repulsion than between
carboxylate and uncharged groups. This is basically because the r^-12 is
not a very realistic potential form and because no polarization is
included. Maybe you want to have a look in

  author =       {W. R. P. Scott and P. H. Hunenberger and I. G. Tironi
and A. E. Mark and S. R. Billeter and J. Fennen and A. E. Torda and T.
Huber and P. Kruger and W. F. van Gunsteren},
  title =        {The {GROMOS} biomolecular simulation program package},
  journal =      {J. Phys. Chem. A},
  year =         1999,
  volume =       103,
  pages =        {3596-3607}

If you still feel that the parameters are wrong, please report back to the

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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