[Molecularmechanics] Re: Some general remarks.

[Konrad Hinsen]

On Wednesday 19 November 2003 05:48, Martin Field wrote:

>    Clearly both problems are important, but
> it would seem to me that tackling the force-field
> problem is in some ways easier than the composition
> problem and that the latter could have a more immediate
> impact in the MM area.

I guess that depends on what everyone is doing. Those who are into developping 
and comparing force fields would benefit most from a unified force field 
representation. Those who are (like me) more into analyzing simulations would 
benefit most from being able to read other people's system descriptions and 
trajectories.

Anyway, there is no opposition between the two, and those who are interested 
in force field descriptions should certainly go ahead and work on that.

> 1. Specifying composition is not a problem unique
>    to MM simulations. Conventions to do so already exist
>    and no doubt there are ongoing efforts as well.
>    How much overlap is there with these?

The biggest effort is certainly CML, which we are trying to build on. 
Otherwise, all I know of is conventions from crystallography. Perhaps Peter 
knows what the current state of affairs is in that community.

> 2. Is a unique convention desirable? Thus, for example,
>    a PDB or a CIF-like convention may be most appropriate
>    for biomolecule people but other conventions may be
>    more suitable in other areas.

I do think that a unique convention is desirable, provided that it is 
realistic. Again, I think CML goes a long way already.

I used to be a CML skeptic, but that was CML1. CML2 looks like a very good 
basis to me.

> 3. Most simulation programs that I am familiar
>    with generate explicit lists of atoms, force-field
>    terms, force-field parameters, etc. when they
>    generate a force-field for a particular system.
>    Most of these can also write and reread this
>    information so that the force-field generation
>    step does not have to be repeated.

Indeed, and a description at that level might be easier to unify than a 
description at the level of an abstract force field specification ("the 
CHARMM force field"), because what really differs greatly among force fields 
is the algorithm for assigning parameters in a particular system.

However, my preference would be to have such information as an add-on (either 
in the same file or in a separate one) to a system specification.

In case you worry about the complexity of the fragment stuff, note that it is 
entirely optional. The proposal I made on the Wiki concentrates on fragments 
because that's where the problems are that need to be discussed. Nothing 
stops any program from producing an empty "template" section and writing out 
all atoms and bonds explicitly, which may indeed be simpler to implement.

However, a file that does contain a well-defined fragment list is both more 
compact and richer in information, so I think it's worth working on that 
approach.

Konrad.
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