[gmx-developers] atommass.dat

David spoel at xray.bmc.uu.se
Tue Jun 17 06:15:27 CEST 2003

On Tue, 2003-06-17 at 16:35, Berk Hess wrote:
> >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.
that may be so, but I want to scale a box to a certain density without
too much thinking, so editconf -density would be a good way.

If we have to choose then I would prefer to have normal atoms rather
than united.

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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