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

Gale, Ella ella.gale at imperial.ac.uk
Wed Mar 29 12:37:16 CEST 2006


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?

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 GROMACS?


Ella Gale
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