[gmx-users] Re: Force field parameters for GROMACS

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 6 10:58:41 CET 2002

On Wed, 6 Feb 2002 Brian.Smith at wehi.edu.au wrote:
>The GROMACS 3.0 force field is based on the GROMOS-87 force field 
>(apparently, Chapter 4 , p47 of the GROMACS manual). The problem is that 
>the GROMOS-87 force field is not described anywhere in the generally 
>available literature - if you consider the GROMOS-87 manual to be 
>generally not available.
>So my questions,
>1) Is the GROMACS 3.0 force field described anywhere else (in 
>particular, the details of how each inividual parameter was determined).
There is an old reference:
  author = 	 {J. Hermans and H. J. C. Berendsen and W. F. van
                  Gunsteren and J. P. M. Postma},
  title = 	 {A consistent Empirical Potential for Water-Protein
  journal = 	 {Biopolymers},
  year = 	 1984,
  volume =	 23,
  pages =	 {1513-1518}
which doesn't cover it all...

>2) In particular, how were the parameters for the amino acids 
>determined? (I've seen in the literature of how parameters have been 
>determined for things like water or DMSO, but not for amino acids).
Basically they were copied from an even older forcefield, and then the 1-4 
(reduced) LJ interactions were adapted until a test protein was more or 
less stable..

>I'm trying to determine parameters for non-standard amino acids, and 
>would like to keep as close as possible to the original detemination 
Try to use analogous groups from other amino acids. There is no "standard" 
way to determine charges (like in Amber) or LJ parameters.

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

More information about the gromacs.org_gmx-users mailing list