[gmx-users] g_msd and make_ndx

[David van der Spoel]

toma0052 wrote:
> Hello,
>      I am looking to measure the diffusion coefficient of a subset of water
> molecules moving through a pore in a lipid bilayer.  In looking at g_msd and
> the -mol option, the manual states that my index file needs references to
> molecule numbers rather than atom numbers.  I was wondering how I go about
> this.  The help for make_ndx is a bit unclear to me.  It seems the selections
> that I make all end up giving a reference to the atom number.  Am I missing
> something here?  How do I get an index file with a reference to the molecule
> number?
> 
> Thanks,
> Mike Tomasini  
> 
If you know which molecules they are then you just write in a text editor:
[ mymolecules ]
3 5 19 23 45 109


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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