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

Frederic Leroy frederic.leroy at urv.net
Fri Jul 1 21:51:54 CEST 2005

Anton Feenstra wrote:

> 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?

sorry for replying you so late. First I thank you for your answer.
Dealing with this AUA model,  a CH3 group is represented by two centres. 
The first one is  that  located on the C atom position on the molecule 
skeleton. It has the mass of CH3 but no interactions are calculated 
between these mass centres. The second point is that which is used in 
the calculation of interaction. It is massless and displaced from the 
mass centre so that the existence of H atoms would be represented 
without treating them explicitely. Then in the AUA model you have to 
compute the force exerted on the mass centres because of interactions on 
massless centres. Indeed only the mass centres trajectory is calculated 
in a MD simulation.
I don't know if this is clear but a publication in which you could find 
some explanations about this model  would be:
Ungerer P. et al., J.Chem.Phys. 112, (2000), pp5499-


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