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

Gale, Ella ella.gale at imperial.ac.uk
Wed Mar 29 13:31:13 CEST 2006

-----Original Message-----
From: gmx-developers-bounces at gromacs.org on behalf of David van der Spoel
Sent: Wed 3/29/2006 12:16 PM
To: Discussion list for GROMACS development
Subject: Re: [gmx-developers] Re: UFF in Gromacs and PBC

> 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?

Well, there is also an extra improper torsion, which is also a Fourier expansion and should be easier to add than the UFF Angle was (I hope as I intend to add it at some point in the future). UFF does cover the whole periodic table. Thus far I have just put in atoms I need for the force-field. The parameters are mostly generated from a set of simple rules. At the moment (as I only need 5 atom types) I have been generating all the parameters by hand, but a script could easily do that part. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20060329/b881d73c/attachment.html>

More information about the gromacs.org_gmx-developers mailing list