[gmx-users] Anisotropic United Atom model and dummy atoms.

Anton Feenstra feenstra at few.vu.nl
Wed Jun 15 17:27:54 CEST 2005

Frederic Leroy wrote:

> Dear GROMACS users,
> my question deals with the way of modelling an anisotropic united atom 
> (AUA) using GROMACS dummy atom option.
> The AUA model for a methyl group is made of a mass centre without 
> interactions having the mass of CH3 and a masseless interaction centre 
> displaced from the mass center at a short distance. The interactions are 
> purely LJ.
> I think that the 3fad dummy atom is the solution using an angle of 180 
> and a displacement of 0.021nm in my case.
> I added dummy atoms in the .itp file, adding them or not to the 
> constraints, bending, torsional interaction lists. I introduced the LJ 
> parameters in the force-field for the dummies and put the two LJ 
> parameters of the non-interacting mass centres to 0.0.
> I do not have any error message during the "grompp_d" stage or during a 
> constant volume run. But the result that I obtained for the total energy 
> is inconsistent. The LJ energy is repulsive, as huge as if the dummy 
> atoms had LJ parameters greater than they are while I am far from a 
> dense state of the system. Thus the converged density strongly 
> underestimates the best one the model is expected to yield.
> Does anybody have an idea where I made some mistake(s)?

Did you look at the pressures in your const volume run? If these are 
(highly) positive, then at least it is consistent.

Setting the LJ parameters to zero may not be enough if the LJ-pairs are 
set explicitly as well. (Check for a [ pairs ] section in your topology 
and/or the forcefield itp files.)

Out of curiosity, what is the use of this CH3 'AUA' description?
Do you take into account the center of mass of the 'real' CH3 group and 
the LJ center to represent the 'actual' CH3 interaction?



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|  _   _  ___,| K. Anton Feenstra                                     |
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