[gmx-users] g_traj -ox -com slight inconsistency

Jochen Hub jochen at xray.bmc.uu.se
Tue May 3 09:57:35 CEST 2011

Hi Chris,

I noticed something similar some time ago. The issue is that the masses 
are read from atommass.dat according to the atom name, if you do not 
support a tpr file (that is with -s a.gro). In that case, sometimes the 
wrong mass is used. In my structure I had a hydrogens called HG (for 
H-gamma), and a mass of 200.59000 for mercury was used instaed of a mass 
of one.

So I guess the only way to be really sure that the COM is computed 
correctly is to use a tpr file.



On 5/2/11 May 2,6:11 PM, Chris Neale wrote:
> Dear Users:
> I have noticed an inconsistency with g_traj -ox -com output when using 
> -f a.gro and either -s a.gro or -s a.tpr where a.tpr was constructed 
> from a.gro.
> There does not appear to be any difference when not using the -com flag.
> The difference is on the order of <=0.008 nm so I suppose that it 
> could be related to rounding and order of operations or precision.
> The same results exist for at least 4.0.5 and 4.5.3.
> Thanks,
> Chris.

Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell&  Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755

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