[MMTK] Auto-discard notification

hinsen at cnrs-orleans.fr hinsen at cnrs-orleans.fr
Thu Jun 22 09:04:31 CEST 2006

On 21.06.2006, at 12:16, Sanzo Miyazawa wrote:

> I inserted a debug line in bonded.c to print 4 atom indices, all  
> atom positions,
> and dyhedral energy.
> The sequence of "4 atom indices", the reference order and
> the way to specify the 4 atom indices,  were different depending on  
> computers.
> Is this normal?

This can happen for improper dihedrals in the Amber force field.

For every four-atom group with one central atom and three others  
bound to it, there are in principle three different definitions of  
the improper dihedral angle. The Amber force field specification does  
not say how to choose one of them (or all of them, or an average of  
the three, or ...) When I asked about this aspect on the Amber  
mailing list, I received the answer that only one of the three is  
chosen, and that the choice depends on the alphabetic order of atom  
types. This is what I implemented, though I consider this  a very bad  
choice for a quantity that is supposed to have a physical meaning.

The alphabetic order leads to a unique choice only when all three  
atom types are different, which is not always the case. If two or  
more atom types are identical, the choice is practically random, and  
might well depend on the configuration of the computer. Any program  
implementing the Amber force field should have the same problem,  
though those that (like Amber itself) define a system with a rigid  
atom order have a better chance of getting the same result on all  
computers - at the price of having the energy depend on an arbitrary  
choice in the system definition (the atom indices).

The only proper solution would be to make the energy dependent on  
nothing but physical parameters. For improper dihedrals, the only way  
I can see is to use the average of all three improper dihedral  
choices. However, I hesitate to do this as it is in contradiction  
with the Amber force field specification.

Note that the three choices lead to very similar energies because the  
three bond lengths are quite similar. The amibiguity in the  
definition probably has no consequences for the interpretation of  
simulation results.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen ät cnrs-orleans.fr

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