[gmx-developers] Re: UFF in Gromacs and PBC

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 29 13:16:12 CEST 2006

Gale, Ella wrote:
> Hi,
> I have just joined this list so please forgive me if I ask anything too 
> obvious. I'm afraid I have many questions today.
> I wondered if someone could explain how bonded interactions across 
> periodic boundary conditions is implimented in GROMACS. Do you need to 
> tell GROMACS that the bonds go across boundaries in the start-up files 
> somewhere, or is it clever enough to figure out that the distance via 
> the perioid boundary conditions is smaller?
Yes that works as it should.

> Is anyone working on adding the Universal Force Field, UFF, to GROMACS? 
> I am interested in using GROMACS to model a slightly different system to 
> that which most people seem to use it for, namely for modelling 
> thioalkane self-assembled monolayers. I have added a Fourier expansion 
> angle function to GROMACS-3.2.1, which is necessary for the UFF. I did 
> this by basing it on the Ryckaert-Belleman's function (to get something 
> akin to a Fourier expansion in theta)  and the angle function to get 
> theta and dthetadr. Would it be of interest to you to add the UFF to 
Yes, but it depends on the amount of work needed. Is it only this extra 
angle function? How about force field parameters? Doesn't UFF in 
principle cover the whole periodic table? How about all possible angle 
and torsion potentials?

> Regards
> Ella Gale
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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