[gmx-developers] atommass.dat

[Berk Hess]

>Hej
>
>I was looking at the file atommass.dat. It seems that these masses are
>forecfield dependent, since they have e.g. aliphatic atoms with mass 15
>(i.e. a CH3) group. I don't  know the history of this but it is not very
>nice... Do we need to make this force field dependent (that means have
>different files for each ff)? But then how do we know from a gro or pdb
>file which forcefield it belongs to?
>
>--
>Groeten, David.

atommass.dat is only used when you do have access to the forcefield,
such as running editconf -density on a pdb or gro file, or running an
analysis tool with a pdb or gro file instead of a tpr file.
This means that we can not make it forcefield dependent.
I guess the only way to improve this is writing a smart algorithm that can 
determine
if there are hydrogens that belong to aliphatic atoms.

But I would say that this mass is not very critical. All gromacs programs 
already warn
that the masses are based on atom-names and might not be correct, except for
editconf and genbox, we could add a warning for those.

Berk.

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